A couple thoughts from way back when I worked at a yacht yard....
The boats that sit around have phantom issues. They come and go. Yours sounds like one. I bought my boat two years ago with the same amount of engine hours as 5 year old ads. And got the same song and dance about how 'she was used just last year....'
Totally eliminate the issues one at a time (starting with the cheapest issues) Fuel line is pretty cheap compared to having someone come down and muck out your tank. You can't always tell if fuel line is collapsing from a visual look. It's more an internal collapse. Get Marine rated fuel hose (not auto zone).
I would measure the fuel line. Replace one side. From dip tube to filter. Then from filter to block. See if this helps. It is likely that a hose is collapsing inside.
Since you have found the dip tube itself to be clear, I would suspect the hose collapsing. It is not unheard of (but again, not on both tanks at once) that the dip tubes crack up the pipe, allowing air to get in. But this doesn't sound like your issue because the engines just die, and aren't air bound (at least not reported here)
You mention a mechanic came aboard. Did they confirm the correct amount of fuel pressure after the lift pump, before the injection pump?
Your issue probably isn't BOTH lift pumps going at once, but..........
One good thing about this. You will be an EXPERT at bleeding your engines after this. A previous comment made by someone was REALLY a good one. If you don't have one, get an electric lift pump installed in each side, with a Tee in the line so you can completely suck out the fuel line and racors of air after a filter change. Makes life a breeze when doing filter changes. I only have to bleed the injectors after I do the on the block secondary filter now. These pumps cost about 30 bucks apiece, and require an extra tee, and a good quality valve.
