Drop me a line before you do the top end as I have the ball hone Eric recommends, for your use.
As far as exhaust, my then new the FMF pipe had to be beat with a hammer to clear the gas tank (partial melting of the bottom) and kick starter, whereas the Turbine Core S/A rubbed the stock-sized tire (a larger tire would rub even more). My second exhaust was full ProCircuit: perfect bolt-up fit! And no tire rubbing.
Also the FMF was pre-stressed at the pipe joint, which resulted in more than one muffler inlet failure; combined with rust, it had to be repaired every two years.
FMF may have a better bottom response (minimum) but it's not worth the poorer fitment and loss of longetivity over the PC. PC seemed to have better top end and certainly better plating.
An after market carbon-fiber guard is costly, although having one would minimize dent repair - recommended. The aluminum ones make noise and are ugly, though functional.
Back to tires, I'd recommend the stock size as optimum because there are times when you want it to break loose and spin rather than hookup, and the geometry stock, if possible. If you can return it for the correct size then do that, though having a larger one for trail riding would not hurt. Put an extra heavy duty tub in with it, especially with the cacti we have around here. I have some very good tire irons if you want to use them.