Hi--I think you are right on the money when it comes to your bite. SHAME on that dentist to start shaving and screwing around with your teeth. That is the biggest no no when it comes to TMJD it makes me furious. These dentists have no idea what harm this can do, and they all think that their way of doing things is the end all be all on the subject. My last dentist shaved some of my teeth before treating my tmjd as well, now 15yrs. later, I am in horrendous shape trying to fix the damage he did to me.
Thelma-Louise is right, you should think about reporting this guy and letting the dental boards know that he did stuff to you that should only be done in the case finishing part of your treatment, NOT the first thing. Never let any dentist change your bite right off the bat. You need to find an excellent tmjd doctor and bring all your x-rays, concerns, (write them down so you don't forget) research in your area, or in the surrounding states for tmjd doctors..and get some consults. If your bite is "off" now, you will get worse, and it will not go away without the proper help.
Also, in my opinion, I think the NTI and splints that don't make contact on all teeth should come with a disclosure or warning to patients when they are given . The dentist's that tell you you can't get an open bite from them are full of crap. Your teeth can shift in a matter of a week or 2. I know, this happened to me as well. Keep researching, and call ortho.'s and dentists' in your area and see who they refer their severe cases of tmjd too. See what names come up over and over, and maybe that can lead you in the right direction. Good Luck!!!! the sooner you get to a competent dentist, the faster you will heal. The hard part is finding the person.
Hang in there------J.