Sounds like low voltage to the ECU causing the running problems; I agree with the others...
* Check all connections, especially ground (get 'em shiny & tight)
* replace battery
Once that's done, if it restarts, check the voltage, both at idle and at ~2500 rpm and see what you get; low voltage at 2500 would lead me to suspect the voltage regulator. (This with the '00 original alternator.) I've found the voltmeter readout on the multi-function display to be close enough for these purposes.
The alternator is inside the primary case; stator bolts to the primary cover, rotor/flywheel is on the end of the crank. They're pretty robust; haven't heard of them going out.
Has your bike had the alternator upgrade? The early bikes had an undersized alternator (~23 amp capacity), and there's an upgrade kit which has a 35 amp alternator / regulator; if you haven't done the upgrade, it may be worth considering, especially if your regulator has gone out. Idle voltage with the original alternator will be in the low 12s, and it doesn't start charging the battery until about 2k rpm; with the upgrade you will get about 14 volts at idle, with correspondingly better charging. It's not difficult to do the upgrade, but it will require pulling the primary cover to put in the new stator.
The indicators for the upgrade would be the higher idle voltage and a different regulator - 23 amp has square corners, while the upgrade regulator corners are rounded, about the same curve radius as a US quarter.
Whether or not the ECU was damaged due to the jump start is sort of a toss-up - you probably won't be able to tell until you replace the battery & try to start it up.
Good luck, and let us know how it ends up...
'99 V92C with K&N, PMRT chip, Vic stage 1 slipons, and engine by Rylan Vos!
Last edited by Colorado Expat; 08-12-2012 at 10:57 AM.
Reason: clairfy wording