As you can never truly be protected other than making sure it's in the contract with your GC who is doing the project.  

They were going to charge too much for the cleaning and make ready, so I asked if I could do it myself, and then they could send me the security deposits.

It never hurts to talk. 

It tries to do too many things and poorly at that. 

So, you may be able to get your money back at least plus some and position yourself better. 

Do you have any properties are areas of NC that you specialize in?

Do not negotiate anything with him.

@Brittney Yang surprisingly I have found that I can have glue down LVP installed by a local flooring company, we use Artisent Floors, https://artisentfloors.com/, for our local renovations and they are awesome and they can do it for less than what I can buy the product for at Lowes or HD even with my 10% military discount! 

Quote from @Mackaylee Beach: I strongly suggest familiarizing yourself with the Section 8 program and its prerequisites.

So, now that you got your losses and failures done - and congratulations by the way because I can't think it could go any more wrong - now you can start over.So yes, get those properties sold and do this right this time.