Another Aussie welcome mate.
Well as far as exhaust goes.... As
@CanberraR3 mentioned - it can be reversed. Now about your foot peg clearance - easy fixed buy the best quality rear shocks you can and go 1" taller - factory rear shocks are crap...... If still not enough find a set of foot peg rails from a "standard", this will give you a more forward foot position and more ground clearance, but a little messing about fitting them due to the ABS line for the rear brake.
You would be doing well not to molest the R3X too much - be like a Shelby Hertz Mustang one day I recon.