I had a similar problem that I thought could be the transmission as there was a definite knock and boat would not engage. Read thru tons of posts for people who's boat worked fine and then had a loss of power. Gave it Full throttle and would barely move. Thought it may be going into limp mode, but that wasn't the case. Tried cleaning the MAF, put in new plugs, fuel filter and fuel pumps. Nothing worked. Turned out to be a short in the fuel pump connection. Not sure what your boat's problem is, but rule out the easy stuff before you work on the tranny. Seems that any problem I've had has been related to plugs or fuel pumps. Hope this helps.