I also spoke with our landlord this morning... and he honestly sounds overwhelmed at the idea of potential extensive water damage.

That will require them to do a complete and extensive review.

I have been reading extensively about 1031 exchanges, but using "real life numbers" really helped it click in my head.

I want to rehab the whole exterior with new siding and trim. and remodel the kitchen and bath maybe get some new flooring in there nothing extensive.

If you were to make it a habit, the CRA will catch-on fairly quickly.3) If this is your first extensive rehab be prepared (secondary projections) for things to take 2-3 times longer than you think up-front (this is part of the cost of education).  

I am closing on a multifamily property next month, i am planning on living in one of the units during the month of June to do an extensive rehab on the unit.

Even lease is up, ask to sign for 3 months extension, likely landlord will agree. 

It's hard for me to imagine pet damage that extensive though.I'm wondering if the smell penetrated into the insulation behind the walls at the lower levels and if it's getting into the new / cleaned areas and "reinfecting" them?

The second time was delayed due extensive underwriting review and the UE questioning why my wife is not on the loan. 

Jaison, the LLC is an extension of you since you own the LLC.