its usually that the contacts have unevenly worn and that the gap differs between them.
I use a dwell meter to set the points so they are "timed" together, then I check the ignition timing
Got a call from OT today, saw me in Monton, so he came round in this
so he's now got a Triumph Daytona and the MV and very much still alive
Oh and the Tracker went on one cylinder and its not the coil
OK you never mentioned a modded air box, that will fuck up your fuelling at the top end and it will run lean.
Its a bit scary finding loose stuff and I would be inclined to check every single nut and bolt on the bike before use.
maybe you can look at a stage 3 jet system to offset the air box mod (nit sure exactly what has been done)