Have you seen this
thread? The guy who was having this problem (which sounds almost exactly like a problem I was working on this weekend...) found it was a vacuum leak. Since you've recently done a lot of work, you may have one as well. I could reproduce the "misfire" (or bucking, shudder, whatever you want to call it) symptoms almost every time by cruising at highway speeds on level ground and giving the engine a tiny bit of throttle...just enough to begin to speed up very gradually, but not enough to kick down to a lower gear. Had to leave my brother's house, so I didn't have time to resolve it, but he's going to check it.