We also learned that the house had failed or not received many of Baltimore city’s permits and inspections.

GC never pulled any city permits yet charged me (didn't find this out until the job was finished). 

Just the other day I saw someone had used black sheet rock screws in the hangers on a brand new deck (non-permitted obviously, and not a single lag or any flashing on the ledger board, and they painted it immediately before the pressure treated lumber had even dried out so that’s going to peal in the first year, at about the same time that those sheetrock screws start to rust lol). 

Are soft costs like permit and architectural fees drawable and when are they released?

Built without any permits.  

Yes, this can be very dangerous, we always use a licensed contractor that has pulled the permits.  

Been getting nowhere with zoning laws found online and in the local library for Yonkers (in westchester county) as to whether any permits are needed in order to operate such a business. 

Currently, the contractor is demanding $44K upfront to resume work and complete the occupancy permit, promising to discuss the additional costs afterward.

The main property will be my primary residence.My biggest question is, what kind of foundation would you use, (that is to code and will pass inspection/permits in Charlottesville) that is either relatively easy DIY or cheap to outsource.

It's also nice because we can upload invoices, quotes, drawings, permits, etc all to the individual project we create.