The HOA claims they deal with standing water in the main sewer line by bi-annual snaking of the line.

(still alive and well :) However the paperwork for the Claim for reassessment exclusion for transfer from parent to child was never submitted.

My title company is now trying to track down all his siblings to sign affidavits to clear any claims on the property.

Will that affect my ability to sell it in two years and claimed it was my primary residence?

If a guest ever initiates a charge back there are specific rules that you must follow to dispute their claim. 

At the move out inspection meth paraphernalia was found.  The unit tested positive for meth and was condemned by the health department.  $7600 later to have it decontaminated and replace everything permeable I am wipe...

And just as an aside, to claim a primary residence you would need to live there.

A partnership agreement doesn't have to be in writing, but it's helpful to demonstrate that the relationship was as claimed.

I have the primary residence which generates no income and for the properties which I own, I have done cash-out multiple times so overall my D/I is hitting the max.Is there a way, I can move one of my properties to my wife (we are in CA and she has quit claim all properties before) without any tax implications, to open up my D/II was thinking of refinancing, adding her back, and then again refinancing and removing myself but given we collectively have more than 10 properties, this route will not work.Any other ideas?

Technically at the moment the trust still has claim to the property.