I’m curious to see if anyone has any experience in this sort of subject as if it would be easier to buy a home with a building already on it then ask the township for a permit or if we should continue to look to buy and build. 

DM me with what sort of contractor you're looking for and I'm happy to find out for you. 

I need a checklist of some sort.

Is there an inspection of some sort or do I need to ask the condo association for maintenance records?

Guarantee a note personally sort of defeats the purpose of utilizing a remote entity, at least for the liability created by the note.  

Should I try to have him fill out a W9 and sign some sort of contract since money over $600 is being exchanged for services? 

You will probably have some sort of limit regarding mold/medical, but thee things can turn into a mess, trust me, I manage a lot of units and have done so for almost 30 years. 

These are just a few starting places that could help you sort through your plans! 

I'd refer them to petscreening.com and let them sort out the ESA letter.

I figure if I charged any sort of deposit, they will leave the place dirty enough to justify the extra work to clean it back up with the deposit money.22 houses total.