You are not sacrificing reliability, just opening up the pores, a cleansing, if you will. You are allowing the 50cc to do what it was meant to do.
Just make sure everything is cleaned off before you install the new mani - no debris in the engine!
Get the mani, carb, and exhaust installed correctly (to where it runs a little rich) and then worry about the cvt. I would advise some aluminum tape to seal things off as you install the next part, etc.
This is uncharted territory for me, so I am learning through this as well.