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. The one thing I did notice is that with the bike level and rear wheel lifted off the ground, the rear tire does not seem to be centered in the rear fender, leading me to believe that the powertrain is still off center causing the issue. 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. Any ideas??

 

You might want to try posting this over in the Dyna section. You'll get a ton of replies there.. I would not be surprised if the rear mount is gone allowing the motor to move back and down in the front. Part of the rear mount / tranny could be hitting the frame.

 

 

Pull it out and see if it's rubbing the frame..