For sure can be a key sign but how many actually fill out pre-qual, view, apply etc. 

Your issue is usually resolved by either (i) rezoning the property or (ii) applying for a use variance to permit a residential use in a commercial zone.

I don't think I need to register the property and get a landlord license from the city because I live in the unit but am going to try to get it done to protect me more from the city, I also am not super sure how to start this process, I did make an account with DHCD and apply for the property to be registered to me (I think) and the next to is to get it inspected which will then get me my license to rent in the city.

Plan on havig to apply for a zoning variance in front of their zoning board.

I wonder if we can still apply for the rent relief program for the missed payments from this evicted tenant?

Does it apply to my case - which is NOT eviction, just NOT renewing the lease ?

Personal credit will be a factor when applying for sure, however you should be able to find a loan product that is non reporting and will not affect your personal credit going forward

If you had a solid property manager the rent relief would have already been applied for and received.

I found mine and then applied the cookie cutter approach.  

No change - the real estate professional rules apply to rental income/loss, not capital gain/loss.