Great to get you onboard Joel and Jonathan. Welcome!
Trogdor's concept is a Gentle gifted Bonisagus with a focus in healing so he covered two areas that we lacked before. If he drops I think Joel's healing/longevity concept and Jonathan's Jerbiton would suit very well for us.
That said, an Intellego/Vim expert wouldn't be a bad choice either given that we want to find and examine new vis sources around the island. The magus that covered that for us from the start is leaving.
As my Jerbiton concept is a bit of a trader (or wants to be) is this a problem with keeping the setting isolated?
I would say its a boon - we were planning on trading anyway.
Indeed, the island is on a trade route:
If he can be discreet about our magical whereabouts then trader is definitely a boon to our covenant. We had plans of adding a merchant companion at some point but that won't be necessary with your Jerbiton.
Well, I'm trying to reconcile the early statement of wanting to limit the geographical setting with how far a trader can go, I suppose. Do we make regular trips into Lubeck, running afoul of Oculus Septentrionalis, do we contend with the piracy of Waddenzee?
Japik hates Waddenzee for reasons in his background so he would approve of contending with them on all possible levels even if we are much weaker than them at this stage.
Lübeck and Oculus Septentrionalis I don't know about. I think Prochorus has spent some time there so it might be that he and your Jerbiton might know each other?
Two options for reconciling the limited geographical scope with a trader.
One, we can allow the trading to reach farther, but keep it in the background so that I don't have to develop dozens of locations to hold stories in. He might also work through intermediaries for the farther trading, not owning ships of his own but rather financing shipments of goods to be resold to other merchants. Potential stories would be about piracy (some of his shipments don't reach the island), competition from other merchants locally, possibly smuggling vs the authorities, etc.
The other possibility is that his trading is done at a more local level. By that, I mean trading along the Elbe and Weser rivers, and perhaps as far as the Ems river. Potential stories would similar, though less likely to involve piracy and more likely to involve mundane politics.
In both cases, this would be more mundane stories than supernatural ones. Oculus Septentrionalis is more likely to be a competitor than a client or partner. Trading with the rest of Order would be much difficult, as your magus will not be part of a well-established covenant and thus seen as a less trustworthy supplier. Although a case could be made for being an "independent" not directly linked to the interests of a specific covenant.
So, basically, it comes down to what kind of stories you would like your magus to be involved in?
Unless someone sees a problem, I am going to try to make the Intelligo / Vim magi work.
Some questions:
I saw some reference to an interview. Not sure how that will be handled, but I presume I need to get the design fleshed out and approved first?
Given the cosmology, how much vis does the personal vis source give? I am hoping it is 4. To make it more interesting, I was thinking of a plant that I harvest each quarter, that produces various kinds of vis, but my parens who gave it to me was never able to find the pattern to it. I would also take Skilled Parens as one of my virtues.
From reading the core book, I believe I can take Second Sight as an ability without spending a virtue on it?
Can I take "Understanding Supernatural" as a minor focus?
Given the premise, free study looks like it might be interesting to take. Any objection? (It may turn out to be less useful, but so be it.)
Given the setting, it strikes me that there is probably less interest in, and possibly even resistance to, hermetic breakthroughs. Would Driven to make a Major hermetic Breakthrough" be an acceptable flaw? At this stage he would be trying to get information about all kinds of supernatural phenomena to sue to inspire such a breakthrough.
The interview is basically having the current players (Wits and Bearlord) letting you know if there is anything in your character design that they object to. They are basically focusing on how their own magi would react to your character when they will meet him, although we will not go as far as roleplay the interview. So they may ask questions such as "Why is this magus interested in joining a rebel covenant instead of an established one", which you must answer in some way by your character design or background.
The guideline given on the core book suggest about one tenth what the covenant as a whole can harvest. Based on that, I'd say no more than 2 pawns per year. The exact amount would depend of the kind of vis it provides, and with an unusual frequency it might even end up a fractional number (like 1.8 pawns per year on average). You may try to convince me to allow more, but it will be a tough sell.
As to a source that gives raw vis from a variety of Arts, I don't see a problem with it. There would need to be some sort of theme to the source, so it wouldn't provide vis from all Arts.
If a supernatural ability is selected at character creation, you must purchase the virtue. So you have to take the Second Sight virtue to have the ability.
It is true that a Gifted person can learn a supernatural virtue after play has begun, gaining the virtue without needing corresponding flaw(s) to pay for it, but that is not as easy as it looks.
In what ways would that be narrower than all of InVi?
It could be, but low resources also means few books not much raw vis, so it may not be as useful as in a normal saga. (The same would be true of Book Learner, as fewer books will be available.)
Breakthroughs requires decades of dedicated research. As such, they are expensive in time and resources. A rebellious covenant like this one is an environment that doesn't provide a fertile ground for this. On the other hand, established covenants may indeed be stiffling such research from a just-Gauntleted magus (keeping it one of the privilege of well-established magi). Would a character driven to pursue a Breakthrough leave an established covenant? Perhaps. But there, at least, you would at least have regular access to a lab in which to pursue your research. This might not be the case at a yound rebellious unrecognized covenant, which may struggle to finance its normal operations (let alone the costs of continual research needed for a Breakthrough).
So I'm not saying that it cannot be done, or at least that the character cannot believe it can be done or that it is the better way to achieve it. I'm just telling you, the player, that it's unlikely to happen and may result in sub-optimal choices for your magus -- perhaps even causing friction with your covenant-mates if being Driven (particularly if it's taken as a Major flaw) negatively impacts the covenant.
I'll let Wits and Bearlord weight in on this -- after all, that's excatly the kind of considerations that they would base their decision to accept (or not) such a magus. 
I will wait for comments from the others on most of your feedback (I can happily adjust to make things work). On the minor focus, I would expect that such a focus would not help with detecting or understanding spells, or the form of vis. I would expect it to help with detecting regios and other manifestations of supernatural creatures or forces. I would also expect, if we ever get there, for it to apply when opening an apprentices ares. Is there a better phrasing for it? For detecting Vis sources, and understanding them, I would expect to have to use his magic without the benefit of the focus.
None of Japik or Prochorus are particularly scholarly so that could be a niche to fill within our covenant, but as Arthur says we are very low on books and lab equipment and being a low resource saga it will take lots of effort to increase the amounts of these. So if your character is very focused on research and breakthroughs he might decide he is better suited at one of the bigger covenants where he has at least some reliable access.
I like the Intellego/Vim concept but why not focus on a more exploring theme and have a focus in finding and recognizing vis sources and regios? Not sure if that might be a too narrow focus for this particular saga, that is up to Arthur to decide.
One of the first questions would be why do you seek to join our small and resource-poor covenant instead of one of the bigger ones like Fengheld, Durenmar or Oculus Septentrionalis?
A major Driven personality flaw might cause some problems but if it means you create your own niche within our covenant and it also helps the covenant as a whole to prosper then it could work fine.
I like the suggestions of him being interested in finding regios, and secondarily vim sources. I don't think such a search is clear enough to be a major personailty flaw, but it should work as a minor.
I could not find the information on the covenant aura. I assume it is relatively low. Do we even know what it is yet?
I am working on an additional driver beyond curiosity for why this magus would join this covenant. I will post them soon.
In this thread Quercus found out the general extension and strength of the auras on the island and it's surroundings.
https://forum.atlas-games.com/t/chapter-1c-chasing-the-sounds-of-magic/8453/17
The aura around the tree is 3. There are equally strong auras around the pillars that rises out of the sea some five miles north of the island. We haven't been able to examine them closer yet.
I just realized from the covenant info that Arthur has put together at the top of our forum that we will be losing most of our books when Pytheas and Quercus leaves so I would urge you to ask for some books as your starting possessions that will be brought into the covenant. Such things will also make it easier for Japik and Prochorus to accept the new magi.
I have worked out rough virtues, flaws, personality, and explanation. I think it hangs together. Feel free to tell me if it won't work.
Herman is a covenant-raised Bonisgaus. Affinity for and Puissance with Intelligo and Magic Theory.
He has two problems which combine to repeatedly get him in trouble, which is why his parens (who actually thinks he has great potential) suggested that he needs to get away from the center of things. Herman has a small faerie friend (Herman is not sure what variety this guy is).
The particular problem is that Herman is (minor) compulsively curious anyway. His friend regularly talks him into investigating things he really shouldn't. At least twice he was caught investigating the wards on a magus sanctum. (He had not entered the sanctum or the consequences would have been quite serious.) He almost caused accidents investigating things he should have left alone in his Parens lab. (again, he did not actually break anything, or his Parens would be MUCH less friendly.)
His personal Vis source is a potted plant that produces leaves with vis semi-annually. Examination has revealed that the plant appears similar to a mandrake, but isn't one. It has produce Herbum, Corpus, Terram, Aurum, and Aquam vis in the last 15 years.
At the moment I have given up on the magical focus. I would like to take a minor focus, but I have not been able to construct one that makes sense.
He is personally interested in the supernatural, not in the sense of spells, but in the sense of other effects such as vis, regios, creatures, ... He is focussed on understanding them (which he has been told repeatedly is either impossible or nonsense. )
He is actually very good at explaining things (Good Teacher). At the moment I plan to give him both book learner and free study, even though both may be hard to use.
Yeah, I think the minor focus would have to be something like "regiones" or "magical animals" or somesuch - the problem is, it has to be pretty narrow, which easily lapses into trivial if that particular kind of thing isn't around. On the other hand, if you build your concept around a given kind of thing, then something like that might end up being around 
Do you tell us about the farie or the curiosity trouble? I think Prochorus wouldn't mind, but might say something like Better keep that thing in check. You never know when molestation might ensue.
In the interview, Herman will mention the faerie (sorry, I will name him) who likes to visit him. He will talk about investigating things (in fact, he probably will talk too much about that.) In the course of it he will make mention of upsetting the seniors magi just by looking at things. When asked, he will describe what he was looking at. He will mutter something about "I didn't think that was personal" (which misses many points, but he doesn't get that.) He does have 1 level in the code, so he is not completely oblivious to the rules.
One possibility for a minor focus, if you were to limit it to one realm I would be ok with it. So "Investigating Magic" or "Investigating Faerie" would be fine.
Arthur, that seems quite reasonable. Of the 5 major supernatural virtues, which would you class as Faerie (obviously, Strong Faerie blood, but any of the others) and which as Magic? If a reasonable number of those count as Faerie some of the time (I can imagine that with some it can be either, and you will decided when it matters), then I would take Investigate Faerie as a minor focus, even though he is not House Merinita.