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I believe the 6 flashes after turning on the ignition on an older Twin Cam bike, is the sign of an error code being set (within the last 3 ignition cycles??).....
Check your engine diagnostic codes...
Off the top of my head, I can't remember the process for checking the engine codes on my 2001... maybe do a search, or someone will direct you to a thread with that info..
Did you do the jumper under the seat to get codes from engine light flashing? You can hold down odometer/trip button while turning key and check some sensors, but the jumper will give you flash codes like old school cars.
That being said, I'd check battery itself and connections, don't overlook grounds. Then on to good clean ignition switch and crank position sensor. My bet is battery...fwiw.
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