Have you changed all the fuel filters, injectors, etc...are they running fine but not hitting the RPMs they should? I would imagine a boat that large would be propped to hit max RPMs at WOT considering you run heavy loads. Engine height will only affect a couple hundred RPMs if they are slammed all the way down. Growth on the bottom could effect greatly. But I would start with the simple things first like fuel filters, check for water in them, injectors could be clogged but it would run rough at idle. If it’s over propped then you would be lugging but if the props weren’t changed then I’m thinking fuel or growth.