What kind of speeds are you getting now without pulling anyone? 45-50 is probably the most you will get.
I dont know about swapping the engines out. It would likely be very expensive and time consuming. I think you have a pair of Rotax model 717's, right? Rated at 85 horse power back when they were new.
I have had a 1999 Sportster1800 for six weeks now with the same set up. I could get up to 45mph with passengers, maybe 40 pulling a tube (I have not purchased skis yet). I wont pull anyone that fast (usually I am pulling kids). My wife was pulling me at WOT and dumped me, hitting the water hurt a lot.
The other week I did a lot of what is probably routine or long overdue maintenance. I had to remove the port pump to remove a rock, and put it back with mew Locktite and all torqued down to the original specs. Honestly something that simple made the engine sound better while running. Don't know if it was wrong before, but it seemed worth the work.
I also changed out the fuel lines with new ones and cleaned out the fuel filters, the backfire suppressor (which seemed so gunked up I don't know how the engine got air) and sprayed down the carbs with gumout. Been adding a lot of fuel injector cleaner to the gas tank.
All this work took an afternoon, a lot of which was spent reading the shop manual and figuring out what to do BEFORE taking it apart. Very little money was spent, a few bucks for tubes of Locktite, about $30 for a roll of fuel line. Gumout spray is a bit pricy. The next day I took it out on the river and found it ran a lot smoother and my speed was up about 2.5-3.0 mph.
For pricier mods, I hear a lot about different pitches on the impeller but since mine isn’t broken (yet), I am not considering that route.