When tuning how do you know that you have the right tune? Also if the cat box was left on and the third hole was plugged with just two exhaust pipes coming out, would that hinder the bike?
Only way to know for sure if you have the "right" tune is to put it on a dyno with an qualified, experienced technician. BTW...not sure there is a "right" tune. It depends a lot on what you want out of the bike IMHO...low end torque, better mileage, high end, etc. Not sure I understand your second question, but anything that restricts exhaust flow would not improve engine performance I wouldn't think.