Am I correct in remembering (Away from my books at the moment) that there are such things as difficult abilities, which are harder to learn than regular ones?
If so, could I please have a book and page reference to them to save me the time when I return to my books on monday? (well, my SG's books, but still)
As far as I know there are no difficult Abilities.
There are difficult Arts, which are magical Arts but advance as if they were Abilities (i.e. you need 5 times as many xp to advance them to the same score of "normal" Arts). Their counterpart are accelerated Abilities, which are Abilities but advance as if they were Arts (i.e. you need only 1/5th as many xp to advance them to the same score of "normal" Abilities).
Damn. I was sure there were. Well, that makes my mystery cult idea a little more.... complex.
Mind if I ask what purpose you were planning to use difficult abilities for?
I need some way to represent an ability that is distinctly more in depth to learn, but would rather access to certain things weren't every 2 or 3 steps up it's ladder. It's essentially an ability that exists along side the cult lore to represent the specific knowledge needed to work the cult mystery.
Generally speaking without any house rule, I think that mysteries have their own "organisation lore" ability which does exactly what you want to do.
How to prevent it to grow faster than the character involves himself in the cult?
Just forbid any XP put there, unless specifically given by you as SG (either by quest or only "normal" teaching from the mystagogue, as you wish).
This way, you control the level of the ability, and you can say:
level 1 allows you this and that
level 2 this and that but also this.
etc.
I think it is a common method used for "forest lore" (Tribunal Rhine) and later for a general "nature lore" (HOH MC?) (encompassing the forest lore if I remember correctly) abilites in mystery cults House .
Why do you need official rules? Why not just invent a new Ability that requires x10 of Art XP (or x15 or whatever)? Or why not stretch the related ease factors, so that you'll need higher scores?
At any rate, I too am unfamiliar with Difficult Abilities. ExarKun gave some great suggestions. I will add that you can offer something like a Significanto, a special item that one can learn from. Access to it would be controlled by the cult, thus again allowing the SG to control the Ability's level.
Just rule that you cannot practice the Ability, perhaps restrict the amount of Adventure XP that can be spent on it, and limit the in-play availability (and / or Quality) of books and teachers about the Ability.
You can also give the Incomprehensible Flaw (ArM5, page 55) to the known authors. This is a good trick, because it slows the rate that the PC advances and also creates a story opportunity for a PC (if she does not have the Incomprehensible Flaw), once she starts writing, to become the authority on the Ability.
This is a bit confusing, because that is kind of what the cult Org. Lore already represents? As a general design feature, I would be wary of creating Abilities that duplicate what the players might reasonably expect other Abilities to cover --- because that leads to, out of character, arguments and confusion about which is the right Ability to use in various circumstances.
Also, be wary of creating Abilties that need high levels to be worthwhile --- because the characters who invest in those Abilities become crippled relative to those characters who have XP sunk into Abilities/Arts that have more immediate utility.
The cult requires you to learn another language in addition to the ones you already know, along with cult lore. Cult lore works fine in Latin, where the language is, in modern terms, akin to a programming language, and thus needs to be memorised independently of the cult lore. In addition, to follow one of the 3 paths of this mystery requires you to focus on the language rather than the cult lore, since it relies on comprehension of esoteric texts rather than knowledge of the cult's rites.
This sounds kind of akin to the Bjornaer Mystery Cult which to varying degrees uses Bjornaer Cult Lore, the Heartbeast Ability, and Dead Language: Gothic, all of which are of only minor utility in-play. This means that (in my in-play experience, at least) the Bjornaer character is better off igorning his House Mystery altogether and spending his XP on Parma Magica and Arts, and/or following a Nature Lore Mystery instead.
Probably true, but this mystery is designed to appeal to someone of a certain mindset, rather than being a be all and end all to power. Not every mystery path has to lead to godhood, after all 
Absolutely. However, I still advise that if you intend some PC characters to sink lots of XP/time into a Mystery, while other PC characters do other things with XP, that you consider what the PC gets for his XP. It's not so much about power, but about whether what the XP has been spent on is useful and/or allows the character to do new things. Esoteric languages are the classic waste of time --- take Dead Language: Gothic, if you sink lots of XP into the language you largely get to speak to other Bjornaer, practically all of whom you could have spoken to in Latin anyway. It doesn't really make any difference in play.
The ability to make essentially a cross between a virtual intelligence (using a form of spirit magic) and microfiche reader for hermetic magic is what I get out of it. Frankly, it's not a project I expect to complete in Saga, given it's almost certainly a major breakthrough for the first part, and a series of minor breakthroughs for the rest, but it's a concept I've discussed with my SG as something my character might possibly come up with and try to develop. Given that there are others in the saga who's interests mesh with this, making it a mystery cult made the most sense.
Essentially, the series of mysteries allows you to create a 'virtual intellect' which isn't truly sentient, but can perform tasks as if it were capable of rational, logical thought, which can copy its memories, including text it is taught, into a stone 'harddrive'. That's where the language comes in. It's more or less a representation of exactly how good at the compression and encryption process the virtual intellect is, but to create an intellect with a score in this language, the magus must be able to read and write it (it cannot be spoken, as it has no aural components, but it is designed so that it can collect a massive amount of detail despite so it can reduce the space storage takes up.
This is why I compare it to a programming language. In normal language, a syntax error is something your mind skips over, noting it if you're that sort of personality, but generally, baring serious botch with your "English" or "Native language" 'roll', your work is readable. In this case, if you botched it (or the intellect did, more precisely) you'd get transcription errors. While these are unlikely once it's active, due to it's nature as a slow and patient thing (no stress die here) and inability to imagine things, if the magus doesn't know HOW to compress some information for storage, neither does any virtual intellect he/she creates, and thus, you lose quality in a book you transcribe in this manner. Given that the process reduces the quality if you attempt to study it without copying it back out from the storage and re-using the original resonances, it's not particularly a study aid, but more a means of backing up a library so that a fire is less destructive, and allowing more ease in transporting or exchanging lab texts, notes, and books of low to average quality.
So you are reinventing the automata, but for the scribe ability?
Ish. There's inspiration drawn from Automatae, but not necessarily the same concept. It's more creation of a logic engine which can also scribe. And record sounds etc. (It started life as a "How would I store music?")