Six speeds, eh? Sounds like a nice bike!
If electrical stuff happens, it cuts out the spark completely. Could that be the case? I have seen several similar things:
1. The female side of the connectors at the coils can become loose, causing intermittent connections. This is especially true if you have the Dyna/Accel 3 ohm coils, because they heat those connectors more than normal.
2. The fuseholder (main) for the bike may be aged enough that it is losing its shiny finish. This makes it heat up when running, and can cause the system voltage to drop. Check to see if it's corroded, dark in color, or rusty.
3. Since you had it apart recently, check all your ground connections. There are 2: the big one on the engine supports the alternator and starter, while the small Green one (under the seat or at the coils) supports the ignition and lighting.