Yea its a warped exhaust flange. I use a file and file it till it sits flat on the bench. Plus if the pipe and flange is a 2-pieces when Im done setting the bike up I use some RTV copper gasket maker where the manifold and pipe go together so it dont leak unburnt oil all over let it set over night and you will keep the inside and motor clean.
I just put a Coke can shim in my Jet Pro on my scooter Zenoah head piece today, works so good. Cut a 3/4" wide strip a few inches long, wrap the head pipe and try the pipe and cut pieces off the strip till you can force the pipe on, put on the springs.