Ejector rods can be straightened but unless you have the tools (I use a metal lathe and a dial indicator) it probably makes more sense to buy a new one. I wouldn't think it would cost any more than $20 for just the stripped rod. You'd have to add parts from yours on to it.

The mark on the cyclinder you describe is appropriate. Sounds like a correct cylinder to me. Maybe your ejector rod is the root of the problems.