They're about the same hp - 62 ish. I've never closely compared the two pipes, but they look similar. They're both piston ported, no reeds. The free air came with 32mm carbs, I believe the Cougar came with 34mm carbs. The fan cooled version is a little bit heavier, but not much.
Porting is the same. The Cougar uses the same flat style head gasket the older four port fan used rather than the copper recessed gasket of the free air. The Cougar has a beefier crankshaft. Cylinder-to-crankcase bolt patterns are the same.
I'm not sure how detailed you want to get, but those are the differences I can think of right off the top of my head.