check engine light goes on and off. noticable shaking in car at idle

try changing your fuel filters. seriously i had same problem and that was the fix.

That's strange that a local shop can't scan it. I think it's an OBD 1 system . . . you should seek out a BMW or European specialist in the area. Any competent shop should be able to help. You have some sort of complex driveability problem, and you'll need an experienced diagnostician to track it down.

I have a 2003 540I with 69000 miles. I had the same problem and it was a number 2 coil misfiring. I have a friend thats a bmw mechanic and he fixed it for me.

Run the car for a bit, especially if the car was jump-started with one of the charger kits. A lot of times the vehicle will have to sync before the check engine light goes off and the rough idle stops. I had the same thing happen with my 1994 740iL. Runs fine now.