I plan to have a structural engineer inspect and make a plan.

Although I understand the moratorium is currently scheduled to end on June 30th in many parts of the state there is always the possibility that it could be extended or re-instituted at some point.Has anyone found a way to structure lease agreements for new tenants in such a way that the tenants waive their right to the eviction moratorium or would otherwise be held responsible for unpaid rents during the pandemic (other than rent relief assistance)?

As far as the property tax implication goes, you're talking about two attached structures, therefore should be one parcel- not having two sperate tax bills it seems. 

If this hasn't been structured properly, you will end up with an adverse tax effect. 

is there any legal structure can that protect me in this worst case scenario?

Depends how you structure it.

Overall, my goal is to JV on, and eventually partner with a GP to syndicate, a parking lot and/or structure by year's end.  

@Shlomo Koheler A burning question I have is how to structure those deals with a (very) distressed property?

How should I structure contracts with lenders in order to keep it fair for all parties involved?

We went under contract for 25 units total, but after inspection, dropped 9 that had severe structural issues we were not willing to take on.