We couldn't reach a compromise, so finally I made the difficult decision to sell the place and give them 100% of the proceeds back.

These carve-outs are typical in commercial real estate loans, including those backed by Freddie Mac, and are designed to protect the lender without necessarily compromising the loan's non-recourse status under IRA rules. 

They will scrutinize your material, layout, and contractors. 2nd, if any layout deviates from the original plan, you have to find a structural engineer to prove to them the change won’t compromise the structural integrity of the building. 3rd, your finished materials especially flooring must meet their sound proof standards.

Hopefully they will be willing to work out some sort of compromise or maybe you bring in one more partner to bring the deal back to good standing.

Maybe there is a compromise.

I would definitely go with a "one-trip" container and one with a higher head height; but if you don't live near a port, you will probably pay more to get a "clean" container.You need to consider that every time you cut a hole in the side, you compromise some of its structural integrity and you'll need a structural engineer to certify your plans.  

Tearing up and paving the woods and grasslands compromises the natural systems that rapidly return water to the atmosphere, increasing the likelihood of future floods for miles around.

Could the neighboors compromise the process?

That might be a good compromise for your situation.

Chicago is an awesome market to invest but you have to be willing to compromise on cash flow in the short term, especially if you have to be close to downtown.Hope that helps and happy to talk more.