I would stay clear of starting fluid, maybe propane
If it wasn't so hard it would be nice to see it on a dyno. Its either not making enough HP or I'm back to weight, drive ratio, prop pitch and you've said those haven't changed
4.3 sat for 2 years and found water in oil
If it didn't rust up everything inside your golden, but most likely the motor is toast. Change the oil and fire it up if it will. Run it a while then, check for water and if good change the oil again.
I don't have a 4.3 GS wiring diagram but do have it for the GL and the 5.0 GI and GS. Neither show a Red/Yel wire feeding fuel pump but no biggy. They all show the ECM applies a ground to the FP relay to turn the pump ON.
Only the GL uses the ALT to keep power on the FP, but all EFI motors...
Two filters will help with keeping fuel clean but also can cause the pump to work harder. Many folks like the Racor see thru drainable filters but they are not allowed on a gas motor, diesel ok and Outboards.
Have you tried opening the gas cap when it dies to see if your drawing a vacuum on...
The booster pump was installed on early Gen cool fuel. This was done to help keep more fuel pressure feeding the cool fuel pump. Original cool fuel only used the one pump.
The VST is feed by the mechanical pump so no need to add booster. The Mech pump is doing the same thing. The issue is...
Compression tells if the motor is healthy. New motor should be 150 psi, as it wears it can get lower. The lower pressure gets the less HP the motor has. Test will not show if there is a clogged exhaust
You mentioned one motor gets warmer then the other which can mean it has a blown head gasket
The trim fluid should stay at the same level if the drive is full up or down. The pump just moves fluid from one side to the other. With you going full up and its at Min then you need more fluid
Those are iridium plugs and don't try to adjust, the thin coating will crack
You have the correct plugs for the motor
Advance is good
You have done everything correct. It should be producing enough power if it was rebuilt correctly.
Don't think I asked this before, but look for the casting...