2003 Honda Accord 2003 Honda Accord EX - Idle problem, shif

Shakes or Wobbles problem
2003 Honda Accord 4 cyl Two Wheel Drive Automatic 113K miles

I have a major issue, and my mechanic, and myself can't seem to figure out the issue.
It all started when I had my brakes changed for new ones, which was done incorrectly. Which cause this major down hill turn of events.
My check engine light has been on for several months, and I am continuing to have the same problem.
When I have the AC on, and I am stopped at an intersection, or just warming my car up in the morning, it idles VERY low, and has stalled a couple of times. Also, when I am driving (with or without the AC on) my car is shifting very hard, and has a difficult time going from gear to gear. The engine is also reving up when I start it, and it sits in park.
I am very frustrated, and worried that it might be a major issue. The code that kept reading from the computer, was something that couldnt be read on a general reader.
PLEASE HELP!