The big ticket items were obvious so no real surprises. 99% of the time when you go over budget it's usually because you change plans mid flip or something is uncovered during demo (rot, plumbing issues, structural and so on) .

You couldn’t even touch a complete demo and lot for under $200k in that area.

It sounds like you have $107k for demo and foundation work. 

During demo of the old plaster walls and ceilings, the contractor neglected to put up any plastic to protect the dust from travelling to other parts of the house.Luckily that was day 1 of the project and we were able to correct the issue and realign our expectations.

The City has a deomlition order on the property but can not afford to demo it. 

Demo is done, roof is done, framing is mostly completed except finishing one staircase of two and subfloor of one unit (2 unit conversion from SFH).  

Welcome aboard @Albert Yang

Your GC, when asked what it would cost to repair the floor, quoted you about $12 per square foot for demo, removal, new-floor installation, new stain-grade trim installation, finish-in-place.

About the only people I'm willing to pay hourly are my demo crews and my carpenters, and that's primarily because those are two things that are very hard to estimate by the job... sometimes a piece of lumber just needs to be haggled with for a long darn time before it gets 'just so', and a master carpenter won't be able to leave it alone until it IS 'just so'

Basically, you're paying for the labor of demo and the fill dirt, which I can't imagine is more than $1000-2000.Like I said, just making stuff up...no idea if this would work or not...