I was originally looking at using jet ski power for my current build but after some research found the following drawbacks:
1. Flat bottom boats don't offer a good surface for the intakes to get clean water, as soon as a flat bottom gets up on plane it gets out of the water and you're starving the jets for clean water.
2. Jets ski jets are pretty bad for efficiency, you have the poor fuel economy of a 2 stroke combined with the inefficiencies of a jet. Expect your flat bottom boat to be very expensive to feed on the water. You could probably feed a big block inboard for less $.
3. Jet ski motors are pretty notorious for their short lifespans, expect to rebuild one or both motors within short order if not before you put them into the boat. Jet skis get ridden hard and put away wet. Most manufacturers are pulling a lot of HP out of a small package to begin with.
Usually people take their jet ski out for a rip that lasts less than an hour and they don't really notice the poor efficiency of the drive setup because they don't really use them much. The motors last because they don't really get a lot of hours on them. A fishing/runabout boat generally gets used for hours at at time, you're talking about using two jet ski power trains so it will be like feeding two jet skis at all times, expect a day on the water to cost a few hundred dollars in fuel. That is comparable to running a big block attached to a berkley jet setup, except the big block will get you moving 20-30mph faster for the same fuel. Another limitation you will be stuck with is weight, most skis are considerably lighter than your boat is going to be, this means the impellers in your ski drives are probably not the right pitch and added stress on everything.
Jet drives generally deliver 2/3 of supplied power to the water. Meaning that a well setup prop will convert 33% more power to into thrust than an equally setup jet drive. So with a jet you're throwing away 33% of your potential speed and 33% of your fuel to get 66% of the potential performance of your motor.
As has been said it takes a specific hull design to successfully accommodate a jet ski heart transplant. Without significantly redesigning the hull in your boat you will probably find you have a boat that is pretty slow, terrible on fuel and expensive to maintain. You should really be grafting the bottom portion of the ski hulls into the bottom of your boat, just to feed the drives with water.
If the point of your project is to do something cool then I would build a custom inboard setup using whatever power head you want, coupled to whatever drive you want. If your project is to use a jet for the ability to run in sketchy or shallow water then I would hunt for an old donor boat with rotten floor and a running V8-berkley setup, this will likely be cheaper than the donor jet skis you are gonna buy. If you want to really do something cool that will run in shallow water with the older hull you have then l would build a custom inboard surface drive. I would power it with an older outboard power head that can turn high RPM and fab up the rest, or use an already marinized V6-V8. Locally I have see 2 running merc tower of power motors with pooched gear cases selling for a couple hundred bucks and complete running setups for a couple hundred more, buy the motors and sell the gear cases to pay for your customizing of the power head. Then all you gotta do is build your drive setup, no oil pan means the motors can practically lay on the floor of the boat with the crank shaft maybe a 4-5 inches from the water, couple it to a custom surface drive and you're laughing. Sounds like a lot of work but I bet its less to setup than the jets.
