You should really be using the muffler cap. You can easily make some changes to the internals of the muffler so that the cap doesn't restrict it too much. Exactly what and how depends on which of the at least two types of muffler you have. If you have one tube inside with a bunch of holes in it and one threaded hole at the end for the cap bolt, you can make a big hole next to that thread hole. Also with both types of muffler you can shorten the internal stinger (the little pipe in the cap), just saw a bit off the inside and try it out.
It is difficult to set up a carb when you have an important part of the muffler missing lol.
Idk about the MZ65 pipe. I know that you can get at least 8000rpm and 37.27mph out of the stock pipe (with the cap on) and stock jet in the NTTC carb. An offset magnet key will help smoothness at high rpm probably make it faster too, at the expense of bottom end.