@Bryan B. I feel very sorry for you. I had to handle a similar issue here in California for my parents. The guy is actually on BP... are you reading this Darryl? The so-called contractor was doing work for my parents. I stayed away from the project because it was their home and they had worked with him on past projects. Long story short, his contractor license was not valid, there was no written contract, there was no timeline, there were no permits pulled, the list of issues goes on...
Once I got involved, I got the project permitted and completed. The legal portion took a long time, but I won and my parents received a good-sized settlement. I did have to threaten a lien on some properties he owned, but the check did finally show up.
Here are the basic steps I took:
1) I handled all communication via email. Anything that was discussed in person or over the phone was verified in an email.
2) I went to the city and I was honest about the situation. They could have really dinged me on the permit issue with fees and penalties. But they worked with me and I got my permits in place.
3) I went direct to the subs. They can be your best allies in getting your project completed. Assuming they are professional, they will work with you to get things done correctly. I am not sure what the process is in TX, but I asked all subs for the release of lien notices upon direct payment. Basically, I took over as the GC.
4) In parallel to the above steps I interviewed new GC's and I eventually brought somebody else on board.
5) As a third rail, I engaged with a real estate attorney to start the mediation process. We thought he would take our offer to pay for materials already used and we would move on. However, he fought us through the contractor license board and the court system. In the end, we moved from offering to pay a few thousand dollars to receiving a six-figure check.
The point is that you need to build a case. You give a crook enough rope and they will hang themselves. Document everything: dates, times, who was present, emails, text messages, checks cashed. You need to document, not just the above items with the contractor, but with the subs, the permitting office, onsite workers, everybody.
Dishonest players understand that the legal system is not built on right vs wrong, it is based on who can handle the pain of time/money lost in the fight. Only at the end is a win or loss decided, most individuals will cave-in before reaching the final verdict and the dishonest guy walks away.
I have had to fight 2 contractors in different cases. But they both tried the same thing: drag out the process and see if I would just go away. Both times I won because I was in the right, but more importantly because I had the documentation to prove it.
You have 2 immediate jobs: get the project done by somebody who is competent and make sure the other guy knows that you will go all the way in the fight. Never go into a fight half-hearted or you are guaranteed a loss. This is going to cost you time and money. The money should come back if you win in court or negotiate things in mediation properly. If you don't have the time or money, do not let the other guy know that. Never show your weakness in a fight. I sincerely wish you the best of luck. Don't leave us hanging, let us know the outcome when you get things all sorted out.