You say it only happens in 2nd and 3rd? I'd check your U-joints first too. Not a hard thing to do, and EVERY time I have a vibration that occurs in gear, I check my driveline first. You could have dried out the needle bearings or broken a bearing cap on one of the Us while you were off-road. Check the slop in the drive and then pull it down one end at a time. The two times that I've changed my Us it was doing exactly what you descibed, nothing in first gear but a terrible jiggle in second and so bad in third that you didn't want to go to fourth! Good luck and let us know.
Sully '84 CJ7 Laredo 258 w/HEI