The actual angles that are set by the doublers are what you have to worry about. Most of the time the fuse is built to provide a little bit of downthrust, and a little bit of right thrust to account for torque. So....if you look closely at the front of the fuse, from the top down....you'll notice the right doubler will seem a little shorter than the left one. This is to provide the right thrust. Just make sure when you do your cuts the firewall "sits" the same in the front of the fuse as it did before you made the cuts. This can be accomplished by "shaving" the same amount of each side.

The cowling I wouldn't worry about too much if all you're talking is a 1/2 inch. If it's a straight back shot then the thrust wsher should come out in the same place...or close enough. The cowl on a cub you should be able to fudge a little bit

Did you build this plane already? Are you building it? Did you cut glue the doublers to the fuse sides yet?