f it were me then I'd run the thing total loss. The stock NSR battery will run for at least half an hour, so I doubt you'll have problems there unless you're endurance racing.
If you go total loss then you can lighten the flywheel by turning the outside diameter a little, and also remove the magnets from the inside. Would be pretty good in a shifter Kart I reckon.
MC21 PGMIII would be a good choice, or an F3 PGMII. The F3 PGM offers more advance fom standard setting, but if you're going with Meth then you'll be needing a whole lot more I expect.
Block the GPS sensor hole and wire it up for third gear. I'm running the TPS at WOT on my 300 (38mm carbs) and it runs without trouble. Don't just turn the TPS up to what appears to be WOT though, you'll need to measure the resistance accross it first while it's still fitted to the carbs, and then reset to this measurement with the TPS off the carbs. Alternitively you could wire up a 5K potentiometer in place of the TPS and have a fiddle while you're on the hop.
The harness can be stripped pretty bare for race mode, especiually in total loss spec.