I was just thinking that the only parts not replaced or bi-passed from your tests is the tank itself and that first internal line, so it must be either of those. It would be good to eliminate that line as a possibility before cutting floors or tanks.
I assume you have bi-passed the fuel filter/head etc. It would be disappointing to find there was something solid (like a dislodged piece of the old fuel lining that was breaking up) that is jammed in the head at a bend or something. Possibly sufficient to restrict flow from time to time if it moves. But maybe its lodged sufficient that it does not clear through.
I guess, given it is intermittent and seems to clear itself for no obvious reason, you would want to be sure you really have eliminated all possibilities. For example, when it ran fine on the jerries, were you using any part of the existing system? If you did, you would assume that part of the system is ok. But it may not be the case. By the time you connected in the jerries, it is possible the original system may have come good again if you simply reconnected it, it may have then got you home also without trouble. I guess just because it all ran on them doesn't necessarily prove the problem was back in the system from there.