On THAT PAGE they mention something interesting about "reports of the ignition coil bracket losing it's electrical bond (ground) to the frame. An easy solution is to run an additional ground wire to one of the coil mounting screws." - any thoughts?
all XB coils are dual-fire models and are NOT grounded in any way, shape or form. they work precisely the same as all old school automotive coils which were NEVER grounded either. this style coil is ball point pen simple. primary windings receive constant voltage....secondary windings receive a "trigger signal" which collapses the windings sending a high voltage spark out the tower to either a spark plug as in the buell case....or to a distributor cap as in the automotive case.
i'll also note THAT PAGE plagiarized the info directly from me. the dedicated wire mentioned does NOT ground the coil. it merely uses the rear hex cap coil mounting bolt to tie the left frame rail or negative battery cable directly to the motor as an additional ground source for the motor components only.
i know very little to nothing about ecm programming....afv values....and the like but i do know this: you have a serious electrical problem and it's all inter-related. note this: the coil is triggered and signaled by the ecm.....so is the fan....so is the dash assembly. are you absolutely certain all your grounds are pristine and your ecm is a known good unit? have you tried another ecm? have you performed the warm motor "ecm and harness wiggle test"? this has the flavor and essence of both bad grounds and some sort of terminal fault within your ecm.
know where all your grounds are located? if not let me know.