I have !always! found that the back of (used!) cox reed crankcases are never flat- so i layout a sheet of p600 wetand dry on glass and gently lap them flat. It never ceases to amaze me how much material needs to come off. it is also a good idea to countersink the screw holes very slightly too.
An air leak between the backplate and crankcase could cause running just as you described.

J.M