2nd vote for Millennium. They reconditioned a YZ125 cylinder that was gouged in 2 different areas. Cost a whopping $210 for stripping, welding, and replate. The cylinder looked better than a new one. Quick turnaround time too.
You can either send them a new piston with your damaged cylinder or they will sell you one.
You will need to remove all the studs and other steel bits from the cylinder. When you get it back, take the time to clean out all the threaded holes before re-assembly. The blasting media they use gets packed into the holes, making it impossible to properly tighten the studs, PV covers, etc.