I have a 900 Sei. Other than the alternator being in a different location, I think the charging system is similar to the 750.
Seems your alternator output is reduced, but not failed altogether. A total failure is preferable in some ways because it's usually caused by something simple such as a blown fuse or disconnected wire.
Partial failure is not so simple. Possibilities include a shorted alternator winding, blown diode in the rectifier, bad regulator, or something I haven't thought of.
Only way to find out is to dismantle and test everything.
The regulator rectifier (on my bike at least) is an old fashioned looking device that's not housed in a finned aluminium case like modern units. You can actually get at its innards and test components (like diodes) individually.
Only link I can make between a charging issue and a misfire is the battery getting too flat to maintain an adequate spark.