I recommend leaving the TPS untouched. There are 5 engine maps that the TPS uses to advance the timing. Without the TPS, the only engine map used is WOT. Which is fine when you're running the balls off of your bike...but I've found the TPS makes the engine less twitchy at the lower throttle positions.
As far as the R/R: I cut out all quick connects and used dedicated 8 ga. marine grade pos & neg leads from the battery. While I did not solder the connections, I used exterior grade shrink tube - twice. Between the R/R and the generator, I cut out the quick connect, shortened the leads on the R/R side (they are a lighter gauge) and shortened the run as much as I could (ran the wires under the motor instead of over, back, down, etc.).
The only other possible upgrade is to dig into the generator and see about better brushes - and to run heavier wires from inside the generator back to the R/R.
My only regret is that I didn't take a definitive reading @ 1000 rpms before the mod...so I can't really attest to the actual improvement.
It is on my to-do list this winter to dig into the alternator...I don't know what it is about this bike, but I sure do love taking it apart!
