OK, are you saying the engine runs OK with the hood off, but messes up with the hood on? You have replaced the fuel pump and it acts the same way, correct?
If indeed the engine runs poor with the hood on, it probably means one of two things…
And exhaust leak under the hood…This should be fairly obvious, black soot/oily residue, noisier due to exhaust leak…
Plugged up air inlets….I think the air inlets are under the hoods lift handle, thin little slots back under there. Perhaps there is some paper or tape plugging them up….
And yes, you can not judge much running in the tank. Crazy water flow, and the tendency to breath its own exhaust just adds confusion to the issue…Try it out on the boat, try to make a video if the engine is still misbehaving…