I have thought about that a lot, and could never find an answer to that question

(I also have a boat with a YJ). In my uneducated opinion , I think it would depend on how fast you want the boat to go. If its a general use lake boat I think the Energizer kit will be fine, but if your trying to build a fast river racer type boat I think it would be better to change the whole thing. In my opinion (and I may be wrong) the berk style intake and suction housing should do a better job of feeding the pump because it was designed to work with that style pump. Also the intake upgrade parts, loaders, shoe, rideplates, etc, are available everywhere for reasonable prices.
I don't think I've ever seen an Energized YJ with a shoe / rideplate.
Maybe Tom or Josh (JBP) can give some actual real world info on this .