I got a Scythe Mugen II Rev. B. It is currently installed on my dinosaur socket 939 Athlon.
My new build parts are on their way already including a Core i5 Lynnefield + a ASUS E Pro mobo.
Do I need to lap my cooler before I put it on the new processor?
I wouldn't lap the cooler it's fine and i definitely wouldn't lap my new cpu it voids the 3yr warranty.
If it's something you can't get out of your system till you try it then lap the old cpu and the Mugen and see if it makes any significant difference.
A lapped cooler won't hurt anything on your new install.