ECU flash and a power commander usb II

Yes you can run both, but there are no real benefits. The only reason you would use both is if you already had a power commander fuel map and wanted to say remove the gear and top speed restrictions or turn your fans on at a lower temp with the ecu editor. The ecu editor can change basically anything in the ecu you want.
A power commander can also only control 4 injectors, and the Busa has 8. The ecu editor(aka flash) can control all 8, and a dyno tune with it can be a little better(with a good dyno operator). Ecu ed is also alot cheaper than a pc, at $208.
If you want a dyno tune there also may not be a tuner close by that uses the ecu ed, so you'de need the pc then.
Removing gear/top speed restrictions, turning fans on sooner, turning off pair valve in ecu ed can be done at home with no dyno too, with just a few clicks. Very easy to use and Greg Smith is excellent if you have any issues.
The only thing that stays on the bike with ecu ed is a 2 wire jumper from 2 empty locations in the black ecu plug, and 2 empties in the black yosh connector. You then plug ecu ed in only while in use. The jumper harness can be removed if you like too, although there's really no need and it makes it easy to make any adjustments in future.
You can also buy a bench flasher for $75, you just take your ecu off the bike and plug it in to ecu ed and where ever that has a home 110 outlet.
I'm no tuner, but ecu ed does alot of cool stuff without you having to be.:beerchug:
 
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