hey dave,
i'm no expert but manually guided wide-field photos are among my favorite pastimes. i would suggest that you drop the f2.8 down one or two steps. i generally get better results around f4 to f 5.6 for a 50-55mm lense. especially with an exposure over 1 minute. also i think you are correct in assuming your alignment is off a bit. and probably one or two things are happening to cause the jumping around problem. either the bolt is warped as you say or there are some burrs om the threads that need to be filed down. but i suspect your motor is pulsing just a bit or it is introducing vibrations into the whole set-up. try a manual guideing session a couple times. and check out my eq (barndoor) tracker. maybe get a few pointers.
http://www.iceinspace.com.au/index.php?id=63,373,0,0,1,0