The issue is the wood floors.
The wood floors versus carpeting is the least of your worries. You're putting so much emphasis on the flooring material in trying to find comparables for a market reaction with the different flooring...... you're wasting your time here. Especially,
since wooden floors are not allowed in the subject complex's declarations. So, it becomes a cost to cure issue. If you don't have a cost guide such as Craftsman or Marshall and Swift, go to
www.homewyse.com, enter your ZIP code, and get a free estimate on how much it would take to put carpet in that second level.
Whether the garage was there or not isn’t the entire issue.
The converted garage, in a condominium complex which has declarations IS your major issue. If this was an SFR, you would have a lot more luck finding a market reaction to non-premitted addition / alterations. Just like the carpet issue, you are NOT going to find a condominium sale with a major non-premitted alteration. Your best bet is to find a fixer or two.
Again, it becomes a cost to cure issue. The conversion back to its original intended use is going to be a lot harder to estimate. The Craftsman cost guide or Marshall and Swift would do a lot better then Homewyse here.
On both the carpet and garage conversion estimates, you're also going to have to include an entrepreneurial incentive % that's typical in your area to take the projects on. The proof of the cost estimates and the entrepreneurial incentive is the sale of the condominium itself well below the other sales within the complex. You're just going to have to lay that all out in the appraisal. Complex assignment on top of legal proceedings. I hope you are charging accordingly and gave them your hourly rate to be in court.
Good luck.