I'm interested in this as well. I installed my BD MM (rubber) in my '01 XJ about 2 weeks back. Tightened up the frame bolts pretty tight and snugged up the thru-bolt wrench tight as well. LOTS of vibrations upon start up. Sounded like a poor running diesel almost... So I backed off the thru-bolt nut 1/2 turn and it is better, but still quite a bit more vibrations than OE. I think I may back them off just a bit more and see if that does anything. Even though I added blue lock tite to the thru bolt, I'm afraid if I back the nut off too much it may eventually come off all together while I'm driving. I also don't have the time to visually check that nut each week.
Thinking I'll have my wife sit in the XJ while I back off the nut a bit and see if she can tell if anything changes. She actually rode w/me this past Sunday for the first time since BD MM installation and she thought my jeep was running really rough or something was wrong. :\