I’ve tried everything I can think of now and still can’t find the solution. I have an 01 fxdxt that I can’t seem to get the alignment right on even though all the measurements line up. Recently a friend and myself did a camplate/cam/oil pump swap on it and all was fine prior to doing this. When we were buttoning everything back up, I noticed that when trying to reconnect the top stabilizer link, it did not line up as it did before. At the time, I used the handle of a hammer between the motor and frame to push everything over so the top stabilizer bolt would go back through without adjusting the link itself. Fired it up and all was well other than some extra vibration through the footpegs (I could feel the powertrain hitting the frame somewhere). At first glance, the space between the front header pipe and frame had gotten smaller and I thought that’s where my issue was, bad front motor mount. So I swapped that out and the gap did not change, nor did the vibration. Next step was to do an alignment by the service manual. Followed all instructions, adjusted link so that the bolt holding the link to the motor bracket would go in without having to push the motor to one side or the other, and checked front and rear brake rotor alignment with inclinometer. Measurements lined up. Still decreased gap between front header pipe and frame, still had extra vibration through footpegs. Took it a step further and realigned mounts according to service manual, loosened all motor mount bolts and ran engine for 5-10 seconds, torqued all bolts back to spec. Still have decreased gap in frame and front pipe and still have extra vibration through footpegs. Checked rear axle alignment as well and it is aligned perfectly. I have no clue where to go with this from here as I’ve done everything by the book and am still getting powertrain hitting frame somewhere. Also worth noting that when doing the motor work, the trans and primary were not touched, and I swapped out rear motor mount about 5k miles ago. Any ideas??

Head pipes are seated correctly and I shimmed the front mount a few days ago hoping that would be the fix, no luck. I think shimming it helped slightly but the rubber in the mount tends to be very forgiving

I’ve pulled and checked both front and rear mounts, both look fine and the rubber has not cracked or caved. I shimmed the front mount, done a total alignment a few times now using a method similar to the one you described above. Gotten the bike totally level, checked the angle of the rear rotor and matched it with the level of the front rotor using an inclinometer to measure. I still seem to have the issue, decreased clearance between the front header pipe and frame causing it to rub and rattle at certain rpm’s. I have a new rear mount but did not bolt it up as my current one looks just fine and ideally I’d like to return the new rear mount to get some money back. I’d hate to mount up the new one and still have the same issue, losing about $100 for no reason

Didn’t move the motor other than what pressure would be applied removing/torquing from the head bolts up. I can’t imagine that the problem lies in the top stabilizer, being that it only controls lateral movement and doesn’t do much in the way of supporting the weight of the motor