Removing the engine is probably a lot of unnecessary work, the bottom end of these engines is really strong and seldom needs rebuilding. Pulling the heads to have them freshened up makes sense though - if the head surface is machined, check to make sure your head bolts aren't going to bottom out in their holes when it's reassembled.

Also, if you're planning on a larger exhaust system, keep in mind that increasing the diameter more than 1/4" over stock will reduce the engine's torque with no significant gain in high-end horsepower. Install a high-flow converter and the lowest-restriction muffler that meets your personal noise requirements and you'll have wrung out all the performance you can from the exhaust system.