Alright, Just an update for darthroush and anyone else's who finds this thread with similar problems...
After I replaced the torque struts myself, the problem didn't go away (maybe got a little worse). I decided I was tired of the time and effort this was taking me even though I was pretty confident it was either the Tranny mount or motor mount or both. So I saved myself the time and took it into AAMCO. I think the guy made a mistake when he quoted the time for replacement of both the Transmission mount and Motor mount. Because I got a smoking deal on it. About $400 total for both mounts and labor and also I had a sway bar bolt that was sheared and they fixed as well.
Anyway. When they initially fixed it the guy only replaced the Transmission mount, because he didn't realize where the other main motor mount was. They called me and said it was done. I test drove it and the problem was still there. I took a look at what they replaced and saw that the Transmission mount they took out wasn't in the best shape but It still looked fully functional. I told them they missed the other mount (main motor mount on the passenger side), and pointed it out to them. They said sorry and got on with replacing that one. Later that day they called me back and said they were done. This time when I test drove it it was A LOT BETTER. The clanking vibration is gone and seemed to drive a lot smoother. The sound was pretty horrible, and not something you like hearing from an engine.
So when all was said and done... I probably just need to replace the motor mound and the upper and lower torque struts. Although I'm glad I have a new transmission mount on there that shouldn't go bad for a while.
Like darthroush said, The motor mount seems to be failing point on neons causing some serious unsettling noises and vibrations.
Thanks again darthroush. And I hope this helps someone else.