If you have the ECU flashed and tuned through the ECU via woolich software then no you don't need an additional power commander or any piggyback fuel controller.

R6's are fairly good out of the box just their suspension needs work. Best thing for the R6 or any trackbike is suspension.. Revalve is a good place to start, then off the shelf units then custom valving from off the shelf units working with a suspension specialist to tune the suspension to the way you ride and your riding style.

Also depends on what series you want to run.. St George is a free for all in terms of mods but FX600 has very specific rules..

If I was starting again all I would just go with a "full" system (knock out the cat and create a link pipe with end can) or an off the shelf system. ECU flashed and tuned through the ECU so no need for piggyback. Suspension looked at, braided lines and quickshifter..

Stock MC is good on the R6 and the stock R6 pads aren't too bad either. Many people like quick action throttles because of the shorter throw but having used both I actually quite like the stock throw..

my 2c anyway..