When I first replaced the battery it was running crappy. No pickup, sputtering, etc. I did the TB calibration (pull power to ECU and turn on ignition for 2 min) and that fixed the problem. It's running well now but the idle is low. Is there antyhing I should try?

but you might have been getting fuel and no spark and fouled the plugs...

Are you using new gas? Premium (duh)? I would first go rag on the car HARD, redline it a few times and see if it misses/stutters/etc. Then check the idle. My 2.8 would get a shaky idle when Frank used to have it as he never took the car above 3500rpm. Jorge used to 'fix' it by taking a drive to melborne and back and just beat on the right pedal.