'88 SN speed problem?

My thinking is the exhaust gas leaking into the engine compartment is getting sucked back into the engine and it's not getting enough air. Try running with the hatch open or removed and see if it helps. Just be careful (make sure nothing can fly into the turning belts).

Do you have a timing light? I'd check the timing at idle and around 3500 rpms. That stripped bolt is going to be a problem but I don't think it's the problem.
Unfortunately i don't know enough about your fuel system to be of much help.
Is there any chance you've got an exhaust leak?

Are you sure? I believe I had 1442 which is close and my boat was a hog. It ran fine but it didn't pass 3600rpm. I don't know anything about prop. It was your recomendation to buy the 540 which I am really happy with it.

That prop doesn't sound correct. I have an 87 1:1 transmission. I have 3 blade, 13" prop. Is an ACME 540. When I got my boat I had a 4 blade but it was the wrong size and would not rev more than 3600rpm. Let's see what the pros said.

I'd start with a Spring tune up (new plugs, wires if they look old, new cap and rotor, new fuel filter). Run the tank down then fill it up with fresh fuel and a can of Sea Foam. (Actually, run the tank down, then replace the fuel filter).
When you pull the plugs, look for anything unusual. I'd also recommend a new impeller, oil change and transmission fluid change. These won't help the speed but it's a good idea to start out the season.
See what happens then. If it's still sluggish, dig deeper.
I don't know anything about the Pro-Injection System but the electronic ignition conversion converts the distributor from points to electronic ignition. I wouldn't worry about it. Modern engines use electronic ignition to "tell" the plugs to fire. Older engines used points. Not a bad thing but you had to keep them adjusted, file the points down and check the gap--a lot of people, including myself, consider it a pain.

chessloves is from Lawrence, you know him? the most important info you can come up with at this point is your Wide open throttle (all she has) and post, look at the prop and post those numbers also...alot of guys will spin them up to 5400 and get 35 mph, under propped or the opposite. you may have to much prop and no power to turn it....thats why its important to list your WOT, im sure most will agree. first things first, determine if it is a prop issue or a power issue

Travis,
Sounds like you have a problem due to the PO's thinking his "upgrades" were a sound idea. Is the Holley even "marine" rated? I wish I could help. The best I can do is recommend you find someone that may know something about that Holley system. Remembering back to previous threads, I believe 3 have tried the Holley and I know two pulled them off and went back to a carb.

What WOT RPM's are you turning up? What prop is on the boat?

Can you get in touch with the PO and get the OEM parts back?