I recently switched from a fatty to a trx5, at the same time I swapped from a pj36 carb to a 38 airstriker. I lost a little bit of bottom end power but picked up on the top end and the over rev was much better. I am sure it would be faster in a drag race but took more work to keep moving in the trails. I am not sure if it was the pipe or carb or both that caused the loss of bottom end but I wanted to share my experience.
Also consider that the centermount doesn't work very well with a taillight or at all with the stock airbox.