I suggest you get advice quickly from a qualified CPA or attorney who is familiar with IRS regulations regarding alternative assets in a Self-Directed IRA and thoroughly review your current and past transactions.Even your first investment, as you describe it, has some possible prohibited issues.

If you stay a few days my wife might tell you about some of the therapy sessions she has had to give me as I have continued down this path.

The GC isn't just pulling permits, they're actually responsible for the project.Another alternative is to get a license. 

I would also check with credit unions, they sometimes can help you when banks can't and sometimes they have alternative loan programs that can help you get into a place.

So its great to get an alternative viewpoint. 

An alternative would be to replace the windows in those units with predominate north and eastern exposures first and the others at a later time after you have replenished your reserves.

I hope it all comes to a resolution you can both be at peace with, since the alternative like @Michael Nemeth mentioned can be never ending war.

One of them works at a physical therapy center and has been there 4 years. 

I find it interesting how at first real estate investing and therapy seem to have little to nothing in common, but as you go along you quickly realize how important those people skills, active listening, rapport building, etc. become, especially if you find yourself interacting with homeowners in trouble with things like financial stress, marital issues, loss of a spouse, fear of homelessness...

Its something that the seller is not usually willing to do so I would resort to avoiding PMI by using alternate choices of putting less than 20% down and do an 80-10-10 loan.