Hi Alex!
I have had iontophoresis several times both before I had surgery and post operatively to help with range of motion and swelling. I felt the same sensations you did (burning, redness) but I did not feel any relief after the treatments. I also did not feel like ultrasound helped very much. I think what did
really help from physical therapy was the stretching we did and the fact that the physical therapist taught me about ergonomics and sleeping positions. If your physical therapist hasn't gone over it with you yet, I highly recommend asking, because they are knowledgeable on this subject.. and I know you sit at a computer a lot, so learning how to sit correctly without straining muscles is imperative to your overall well being.
Many insurance companies who
do cover TMJ disorder
explicitly do not cover iontophoresis. In fact, they spell out in the policies that it is considered experimental or not proven to work. This does not mean that it doesn't help some, but basically that there is absolutely no research that has been done on it either way.
I guess my opinion is - whatever helps you, that's great!! Since we're all so different it is hard to compare... as I always say, "What works for one, may not work for another," ya know? But, hopefully some others will weigh in on the subject soon.
Hope you are still feeling better!

stacy