Refine Your Laboratory

So say that I want to build my laboratory in the Ural Mountains.

As a newly gauntleted Bonisagius magus, I have int 3 and MT 5 (includes the +2 from Puissant Skill).

So I walk up into the mountains and start to locate a good site, and find a magical aura high up in the Mountains. As I am prepared for this, I cast my "Conjuring the Wizard's Tower" and ask my few grogs to put in all the crates they have been carrying and I prepare to build my laboratory.

Season 1: Build Basic Laboratory (-3) and I gain 2 xp in magic Theory from exposure.

Season 2: Build Standard Laboratory (+0) and again I choose to pick 2 xp in Magic Theory from exposure.
Question 1: Do I get the Free Structure Virtue: Mountain Top at this point? OR must I refine my laboratory in order to get it (not that it cost any space, but must i have refined my lab to get the bonuses
Question 2: Do I get the Free Structure Virtue: Elevated at this point? As I have my laboratory on the top level
Question 3: Can I get more than 1 Free Virtue per season

Season 3: I refine my Laboratory 1 step, I am lucky and get Highly Organized, but not spotless and choose 2 xp in Magic Theory.
Question 4: Can I now choose a hidden flaw that the Storyteller chooses?

Season 4: I continue to refine my laboratory, so now i have 2 steps of refinement and chooses 2 xp in magic Theory from exposure

Season 5: My pater gave me a good magic theory book with quality 9 and with my book learner merit, I get 12 xp in magic Theory for a total of 20 xp which gives me level 4 with 0 xp

Season 6: I refine my laboratory to step 3 (as I have level 4 with an additional +2 levels in Magic Theory) and choose a few unrelated xp from few adventures (but those are not important here)

Season 7: I install Greater Guardian (Major Supernatural Virtue) as I made a deal with a magic spirit in one of my previous adventures.
Question 5: Is it by this point that I get one or more free virtues that I described earlier in addition to the Greater Guardian or did i get those as my tower was built together fith the first 2 seasons of builing my lab?
Question 6: Do I need to take a season to install a free virtue or will they pop up as i build my lab?

You will have the free virtues dedicated building, mountaintop, elevated and superior construction at the beginning. They are free, and do not require refinement.
However if your MT is 5 you would need to raise it to 6 (for 30xp) not to 4.
The storyteller chooses the hidden flaw, not the player.
Free virtues tend to be issues of construction, but may require extra seasons, or outside contractors. For example, studio or grand entrance will probably take a season of professional construction, but need not take any of the magus' time.

In my example, I used a Bonisagius with puissant skill Magic Theory and hence I need only 20 xp to raise it so that it counts as 6 That is why I take 4 seasons *2xp and then read a book of quality 12 for a total of 20 xp to get to level 4 and then add the +2 from the virtue

Free virtues basically don't take part in the refinement process. You have them if you have them more or less. If you are on a mountain top you have that virtue. If a tower has solid construction you have that virtue. Start posting a guard and you get that. Start bringing your wife into the lab regularly and you get the person virtue. They don't use space in the lab, or take time to instal.
So to answer your questions:
Question 1: You already had it after the first season.
Question 2: Already had it after the first season.
Question 3: You can get as many free virtues as you are able to include in a season. There is no hard and fast rule.
Question 4: Hidden flaw? I've skimmed through that section, but I'm not sure what you mean. Do you mean the Hidden Deficit flaw?

It should be noted that you must have worked in the lab for a number of years equal to the current refinement score to try and increase it. (Cov p110)
You can go from
0 to 1 refinement in the first year (0 years inhabited)
1 to 2 refinement in the second year (1 years inhabited)
2 to 3 refinement in the third year (2 years inhabited)

So your Season 4 refinement needs to happen in season 5 and your season 6 refinement needs to happen in season 9.

If memory serves that is for taking over a lab not building one from scratch. If you build from scratch you are already familiar with the lab and if you spend time improving it beyond the original design you are familiar with it. I think the text says something about it being a rule of thumb.

It only says you have to be familiar with it and gives that as a rule of thumb. The rules for taking over someone's lab are in a different section, if taking over you have to refine it and get either the old score or your MT-3 whichever is lower.

As much as I hate to say it JL, is right about this. I fail to see how you could be not familiar with a lab if you built it from scratch. OTOH, if a lab tech sets up your lab or what similar, I would require the time working in it.