I've heard this story before that Evolution engines don't need to be run in. Don't believe it!! They may (although I doubt it) have been given a quick run at the factory but certainly not run in.

It seems that your suspect engine has just got a much tighter pinch at TDC than the other so just chuck it on the test stand and give it some rich running until it settles down. Use some castor in the fuel too to help avoid any damage and keep checking the pinch after it's cooled down at the end of maybe a 3 to 5 minute run (at full throttle of course).