I'm currently doing what you're thinkin of doin. I chose a 64cc Polini cylinder. I case matched it. That wasn't too rough a task, but it was nerve-racking till I got confident about it. Just start on the fatter chunks first so you can get used to the flow of it so you can be nice and tidy when you get around to the smaller chucks. I put a new DMP teflon stuffed crank in the case. I put new bearings and seals in to replace all the old ones.
I followed the directions in the wiki for rebuilding a Puch E-50. It was easy and super fun. I'd recommend buying a couple tools for replacing the bearings. that 3 jaw puller, and the tie-rod separator. Auto stores here rent out the 3 jaw puller for a refundable twenty bucks, and the tie-rod separator is ten bucks-ish.