I'm surprised exhaust port edges didnt get trashed. It's the rough edges I'd worry about along the ports, something that will mar a new pistol or ring. Leave the dimples top and bottom. They won't hurt anything.
I'd get an FleeBay special, full engine to get it up and running and take this as a porting project. Who opens these clamshells up? Or makes them breath??
I find the 039/390 to be a very capable saw.