I have ran a FMF, Q V2 and Hall #19 on the engine. There was no loss of bottom end when moving from the FMF to the better pipes. The difference between the FMF and the other two pipes is incredible.
You also went from an FMF to a JH, JH does not have a lot off bottom end loss. You will see more bottom end loss with Aaen (Q pipe copy) & Q pipes, especially V-1.