Hi CFreak, Welcome aboard,
The bolt in the muffler is there for emissions testing. If you remove it you simply have an exhaust leak that does nothing for performance. If you want a louder tone you can drill a series of 3/8" holes (6 or so) in a circle around the outlet. Combine that w/ some mild up jetting, and you can get a couple more MPH.
HPI (hores power ignition) in Belgium makes a fully programmable ignition system for Kymcos. I have one on a 50cc, and it is one of the best modifications I have done. (I have done EVERYTHING to my bike).
Depending on what modifications you do a few minutes on a computer with the CDI, and you can set ANY Ign. curve you want./
Their set also comes w/ a 40,000 volt coil so there are no worries.
The aftermarket coils as seen on Ebay Ect. are usually pretty good. They do improve plug life but not really MPH.
Your backfire issue can be addressed by adjusting the idle MIX screw. If that does not eliminate it you may need some re jetting of the main. Usually 1-2 sizes larger will fix the popping, and improve top end speed a bit. Re jetting is something you will want to do if you open the exhaust anyway.