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Did you check all the relay and fuse sockets/connections?
Just pull things out one at a time and check for corrosion on the terminals, sometimes relays can be swapped in position.
A problem between the battery and starter would not change the bike running once started, a bad ground or battery connection would...
I had a similar problem a while ago, dealer could not figure it out. Under the tank is the main harness running back and there are several grounds spliced into two main grounds that come down to the engine case. One of these grounds coming out of the big splice bundle was intermittent, once I discovered where the problem was I took it to the dealer again and told them exactly where the problem was-they didn't believe me or want to believe me and would not troubleshoot the wiring so I picked up the bike and tore into it myself. It is a poor design of the harness because the wires come out of the spice at a 90 degree angle so it is just a matter of time with the vibration and stress on the wire that it broke.
I had this problem for many months, the bike would run fine for days or weeks at a time but then I could get down the road a mike before it would die.
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