I wouldn't remove the top of the head.
To strip off the old paint, some came from the factory that way, Use paint stripper, brushes and such, Or seal the intake and exhaust ports and sand blast it. This will strip the paint.
You say it ran good. Then why mess with it. Step one, if you haven't already get a repair manual. Free as downloads.
As xskid said check the compression. If above 100 psi and even left to right I wouldn't do anything till I had the bike together and rode it awhile.
Actually I would not have torn it down till I was sure of the engine. Ride it a few weeks to determine just how good the engine is. Do a few oil changes, like at 50, 100 and 200 miles. Watch for debris in the oil, strange sounds, how the transmission works.
Putting your bikes year, model and any mods in your signature will help us help you.
But if you must pull it down check everything the book tells you to check. This will help you decide just what needs to be replaced.
There are a few standard things that need replacing. The front cam chain guide, the cam chain.
There are two oil filters, one in the side cover, this one is usually good, just clean and reinstall, the one in the sump, mounted on the sump plate that is held to the bottom of the engine, is often torn. This can be fixed.
I have several of both filters. I have an extra sump plate. I have a clean filter on the extra sump plate, at oil changes I just swap the sump plates. Clean for dirty.
The same with the side cover filter, clean for dirty. This speeds up oil changes. Leave the cleaning of the filters for a time when you are not riding, like at night.
Leo