If the only problem is that the boat is porpoising (hopping in the water) then yes, work on your center of gravity and weight.

If it came with NIMH and you switched to LIPO, is there a low voltage warning that maybe you're hitting? I checked the manual, they don't make mention of it - just that a 7.2 volt battery is recommended. If you're using a lipo without a low-voltage cutoff, you are might run the battery to a level that it can't be recharged.

Is there any way to adjust your prop depth? Maybe it needs to be lowered?