Those deals get better and better every year in a very substantial way. 

Are you working with a Realtor® or a contractor, both can likely solve your problem as the agent will have access to more data and knowledge of how to run comps, the contractor will be able to give you a better idea of repair costs.

Should it be based on the lease value or is negotiating something based on my costs incurred plus time and suffering the better route?

Each Church is different with respect to design but they are generally more expensive to renovate than some other structure types that may lend themselves better to a conversion.

Yes, that's going to make it a lot harder to find a deal that works, but better to do that than realize you're underwater on something.And if you happen to expand your search and are open to Detroit, I'm happy to share more info on that market.

If you pull the equity out through a refinance and deploy it in a new investment, does the combination of the two give you a better return?

Borrowers with higher credit scores are given better rates and more funds from lenders nationwide. 3.

I know this is imperfect but it is better than nothing.2.

Advice from those that know better?

An accountant can explain this in better detail