Pulsing then complete loss of fuel

I have a 1985 2001 that I've restored over the years. A few years ago Jody at FLInboards helped me put a model year 2001 GT-40 motor in the boat because of a block issue on the original 351. The motor has been solid, but the past year I've been chasing a fuel issue. Actually I had an issue with the lower fuel pump a few years back - pieced it back together with spare internal parts.
I took the boat to Jody the last time the below happened (September '18) - caveat: This was pre-Hurricane Michael and the boat hasn't been out since September as a result of the damage to the area. Jody cleaned out the tank and lines, fuel system, etc and verified that it was working, putting only non-ethanol fuel back in (3 gallons). I took the boat to the landing with a fresh battery and it fired right up. Took it back out and filled up with more non-ethanol fuel and took it back to the lake. The problem is, it started fine, idled fine. As soon as I start moving/giving gas it starts pulsing every second or two - almost like air pockets in the lines. I pulled the kids around on the tube for about 45 minutes at ~15 mph and it progressively started getting worse / more frequent. Because I was worried we'd get stranded, and I wanted to see if it was bad gas - I loaded them up and started heading back to the dock. Got the boat (slowly) up to 30mph, pulsing the whole way, and stronger more frequent until about 15 seconds in, it shut-off and wouldn't start back. Temps were fine the entire time (replaced impeller in Sept before I took it to Jody). I've had issues in the past a couple years back with the lower fuel pump as I believe there are plastic pieces that spin around and can break apart. What I noticed yesterday as I was trying to pull the plug, was that the upper black canister (not sure official name) where the fuel filter sits inside was really hot. Leaned up against it and it got my attention quick! I'm not sure where to start troubleshooting, all I know is it's a fuel issue (I think). Any ideas / opinions / starting points are much appreciated!

I have a 1989 2001. I have had with my boat running great then all of a sudden it will slow down and start to die. I thought it was a coil issue so I replaced the coil and the boat ran fine, problem solved , I thought. Next time I took it out started doing the same thing. I removed the anti siphon valve and found some dirt in it cleaned it up and the boat ran fine. Then the last time I took it out skiied a bit and was ready for another run when the boat wouldn't start and then when it finally did it would only idle any attempt to give it some throttle would cause the boat to die. I removed the the anti siphon valve and it was clean so I moved on to the carburater primary bowl and found some dirt in one of the inlets cleaned that up and the boat ran fine. Not sure if this long winded explanation will help and I'm not sure i've actually fixed the problem. Time will tell.

Here's the kit Peter mentioned that replaces the plastic tube.

FCC HP pump repair kit