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is it just plain idling rough, rpm goes up and down, or a combo of both.
a good start would be to clean the TB with TB cleaner, and clean the MAF with MAF cleaner. see what that does.
+1
The PCM could be on relearn as well since you just had it replaced. Scan with the X-Cal2 and let us know. Also, whats the interval like between high and low idle?
The RPM's just go up and down about every 20 seconds or so. Idles at 700 then drops to 400, then back up to 700.
Rinse, lather, repeat every 20 seconds or so...
Read your first post and seems odd this would be the result of an altenator change, though rule nothing out. I agree with the replies on cleaning the throttle body. I had a simular issue with hard starts & rough idle so after cleaning the Throttle body (take it off) my issue was resolved. The difference was huge. Word of caution: Be very careful cleaning the MAF as it is a very sensitive piece.