1, Always a good idea to rebuild. Seals at the very least. But it's your bike!
2, you should match the transfers to the case with a die grinder. Trace the ports on the cylinder and mirror them to the case. Remove the case material so the transfers match better. However much you dicide to match is up to you...chamfer the ports too if they are sharp.
3, yeah air doesn't like sharp edges all the time, I try smoothem in...
That pipe sucks. It's fine for a lil' pep from a stock cylinder, but if you want to get anywhere near to the kits potential get a circuit pipe like clippy says....
15bing is my favorite carb for za50's. But you really want something bigger for a single speed. It's gotta breathe.