The other issue with cruise control may not be related but could be... I may have a short in right handlebar controls. I need to trouble shoot this, my radio blanks out (total loss of power to it), cruise don't work but everything else seems to be ok. I loosened right side controls today and I will pull faring to get to the pins and take readings to see if I can isolate the cause. I despise wiring troubles.
had this same thing happen to mine just after I picked it up (02 FLHTCUI Shrine), first noticed the volt gauge jumping from 14 to 11 and back up. it was shortly after that my gauges and stereo as well as the cruise would quit. the engine light came on, and then everything jumped back to life and the engine light went out. it happened a few more times and then the voltage meter dropped to 11 and wouldn't come back up. the guy had given me a spare voltage regulator and suggested trying that, so when I went to remove the regulator I discovered he had pinched one of the wires in the front motor mount. it must have been hanging on by a few wires and finally broke, so I just repaired it and put it back together. voltage went back up to 14 and the tach/speedo/cruise/stereo cutting out thing hasn't happened since.
so were the issues related? I don't know....I will be removing the outer fairing here soon for a stereo upgrade and will check connections in that area to see if I can replicate the power loss to stereo etc.