88 Baja 240 Sport, 454 MAG

Pulled my boat out from winterization a few weeks ago, put everything back together and put new fuel in. Boat cranked right up on the hose and I let it run for about 5 minutes, everything seemed to be fine. On the water, the boat is fine with a slow take off and moderate cruising (around 3400 RPM). When the RPMs are pushed higher, either with a quicker take off or higher cruising speed, the engine will stall. I can immediately start the boat back up, but I need to give the throttle a little gas, which is leaving me to believe that the engine isn't getting fuel at the higher RPMs. I've replaced the fuel/water separator and have ordered a new fuel pump, haven't installed it yet. I'm just wondering if anyone has any other troubling shooting ideas. Also curious if there may possibly be some kind of damage to the engine as this is only the second time that I winterized the boat myself.

I think you're on the right track, change out the pump and give it a go

Does it pop or just quit?

Sometimes it will pop, but shortly after it will just die. At one point I lifted the hatch up enough to watch the carb (filter removed) and it seemed to back fire through the secondaries (quadrajet carb) then it died.

Did you remove/ replace the filter that is in the carb behind where the fuel line connects? I had this same problem and that filter was clogged causing this same exact issue

Sounds like a textbook fuel starvation issue. Maybe the fuel gummed up somewhere in the offseason. You're on the right track with a new pump. But also check for a line that cracked in the offseason and is letting air in or quite likely your vent is plugged with spider stuff.

I did not check that, Is that easy to check?

Fuel pumps typically either work or quit completely. Did you run the fuel stabilizer through the entire system before tucking her away?

88 vintage 454 Mag probably has the Q-jet on it. Very possible that some deposits built up from fuel sitting in the carb. Almost all gas that is available today has at least 10% ethanol, which tends to invite moisture and cause oxidation in fuel systems. Did you use fuel stabilizer when it was winterized, and did you make sure that the stabilized fuel was fully drawn up into the float bowl of the carb?

I had a similar backfire on my boat about ten years ago, and thought it was a fuel delivery issue. Turns out I had a hole in an intake valve from a chunk of piston that lodged in there. Boat started up and idled fine, ran at cruising speed with no problem, but as soon as the secondaries started to open up it would backfire through the carb. Hopefully not your issue, but a sticking valve after the layup or a weak valvespring could also cause this. It would be revealed pretty quickly with a compression check before you start chasing other things like fuel pumps and ignition components.

One of my engines was doing a similar thing a few years ago. Inspected cap and rotor and had lots of corrosion.
It was fine under a light load at a 3500rpm cruise speed. Push the sticks forward quickly and it would stall.
Push them slow and it would start to miss around 4000 rpms.
Cap and rotor replaced and all was good.