Dealing with a bad contractor

[Leland S.]

After paying my contractor 35k, I found his interior work was pretty shoddy. I already had a few issues with the contractor I pointed out and ask for discounts or refunds, but none were ever given, they just acknowledged my complaint. Once they completed all the concrete, plumbing, electrical, and framing which seemed like quality work as far as I could tell, except for the several issues I took up with them, they got to doing interior work. I got to inspect their interior work mid way through and found so many issues it was troubling. I took pictures of all kinds of issues: damage to most of my new cabinets they installed, electrician replaced a bunch of new lights and fan I had a prior contractor put in, wood trim was installed poorly unevenly cut, drywall finishing looked terrible, the plumbing they roughed in didn't line up with the vanities they knew were there to be measured... among many other issues. 

When I sent them the list of issues they just said they aren't complete the work and to pay up the last invoice (for the work that mostly had the issues) and they will complete the job. 

They have permits pulled on my place now and haven't received final inspections. So I'm worried if they pull out, aside from being stuck with paying for all the damaged stuff, I may have the city say other stuff doesn't work or wasn't done right by the contractor. 

It appears this company just wants their money and doesn't find any obligation to my satisfaction or their quality of work. Several other times they did things wrong they just sent me a new bill with their laborers hours on it and when I asked if they discounted the invoice to compensate for the work not done to spec the first time they ignore or dodge me. 

What's the best path forward where I lose the least and give myself the best advantage? 

BTW, I'm trying to flip the house and have been rehabbing for 5 mo now and want to put on market next month asap. I'm already like 2.5x my budget, hoping to get my money back to payoff my debts.

Experienced advice is appreciated...