I had a similar issue where mine would do that on my w124. I thought is was a electrical issue. I'd put in in neutral and it would stop "most" of the rough idle...so I thought it might be the tranny. After 1 month if it happening, my car would only start up 95% of the time. After being in the shop twice...it was the dual fuel pump that was faulty. We tested both and there both would work off and on.

If your checking your motor motor mounts...tranny mount and flex disc should be checked out too.