I would say just swap out the cylinder unless you got a LOT of porting work done to it or spent a fortune buying one that's already been ported. A new cylinder costs between $15 and $25 depending on type and who's selling them etc.
Then on the New cylinder, if you re drill the holes for the intake and exhaust studs and add in helicoils they won't strip out. Some of the new cylinders come with these studs pre installed and usually a generous helping of red locktite to keep them in place, if you get one that has the studs locktited in like this you can just use as is or carefully heat around the stud with a propane torch until it can be unscrewed, these studs will snap off right at the base if you try to remove them without heating them up first since the red locktite they use has such a strong grip.
If you do choose to replace the jug, these are not all created equally and if you're after performance you will want the type that has the flat transfer openings, not the slanted or cat eye type openings in the cylinder. To help ensure you get the flat transfer type, these are usually called high performance cylinders when sold on ebay and usually cost around $25. Every time I use this type jug pretty much all I need to do to them is remove the casting flash at the transfer opening and sand or file away any nikasil plating that overhangs into the port openings for decent performance, and for serious performance, these are the best ones to do an all out porting job on since they have larger transfer openings and can rev a lot higher.
i'm not knocking the cat eye type transfers either, they do have their purpose... if speed isn't as important as acceleration or torque... like if you have a heavy bike or a heavy rider, these can be cleaned up a little and will pull really hard but top off at around 30mph with the 44 tooth sprocket, these also tend to work better if using smaller rear sprockets. The flat transfer jugs will turn more rpm and make more power, but the torque capabilities the cat eye transfers have can't be ignored either.