@Kendall Mercer I honestly don't even know where to start. If you are having so much trouble with this contractor, then don't use him again or just pay him for what he has already completed and hire someone else.
I don't know what exactly what you had him painted and why, but if say for example you are only replacing part of siding, etc then repainting those parts to the original color is very common. If he only charged you $1000 for the exterior pain and trim, that seem extremely low unless its a tiny townhome. In most areas, you also have restrictive covenants (HOA) so any time you want to paint a property different color, you have to submit that paint color for architecture review. So i'm not sure how those things would get missed unless there was a complete misunderstanding on what you wanted to do and what he quoted you for.
I'm not picking anyone's side, but having those things in writing is important especially for those type of issues. I don't like when people start through lawsuits and courts around. It is not as simple as you might thing and if you have nothing in writing, you might get really hard time with that.
Personally, I think most of those issues for new investors comes from watching HGTV shows. They see investor walking though the property for 5 minutes, pointing fingers on items and then show up 2 weeks later and everything is done exactly as they wanted. That is simple not that case and that is probably why the first property is usually the most expensive to flip because you learn those things.
When choosing a new contractor, i ask other investors or realtors for references and i make sure the contractor is licensed and insured. Getting someone on craigslist with the cheapest bid is not always the best idea. I also stay very involved and hands on when working with new contractors to make sure everything gets completed as intended and on time. Even if you have everything in writing, you still will miss few things.
Also estimates for work are just estimates. Usually getting large items done for that exact price does not happen and its not the contractor fault. For example you might get a new roof big and its 9k. If the contractor is good, they will also specify stuff like "includes 4 sheets of plywood, any additional is $50".. etc. So that you know what to expect and they don't really know until they get started. But if you go though the process you will learn those things.
Or higher GC and they do that for you but its really up to you. I personally like to stay very involved but i also have the time for that.
Sorry if this is not what you wanted or hoped to hear. I had issues with contractors as well, but that was usually because i did not know better when i started and just went for the cheapest quote.
UPDATE:
If you are very unhappy with his work, just pay him for what he has already finished and what you agreed on and then higher someone else. The chances are that if you pay him fair for the work he has already done, he will just move on as well as you and learn from that experience. If nothing was in writing, neither of you have good grounds to go to a court. Also i would not go to a court over small amounts, it would just take me more time and money and the outcome would not even be guaranteed.