ISX "whistling" and shut down

[CoroView Shop]

Good morning,
We have an ISX with issues. It started with the truck being driven into the ditch (yes, on purpose), with low fuel. What wasn't known at the time is that the fuel tanks were full of sediment. Driving it into the ditch allowed the pick up to pull sediment through the fuel lines, where a large portion of it was stuck in the first fuel filter. This resulted in the engine running okay, but will start making a whistling noise in the engine, then quit. Opening the drain on the first filter actually seems to draw in air. Cycling the key a few times to refill the system, and good to go for a few more minutes. What we've done so far:
-- Completely drained both tanks (got about a 1/2 gallon pail of sediment out of tanks)
-- Replaced all fuel lines up to the first filter, including T's
-- Issue was still present, replaced common rail high side relief valve (still had the original), which seemed to "cure" it for about 3 days, then back to the same
The low side pump has good pressure (120psi), but have not confirmed flow (if anyone has that spec, thank you)
The high pressure pump is the 3 cylinder type, and calling the dealer they say that there is an updated 2 cylinder pump that was issued due to the 3 cylinder pump causing engine failures?
Currently, the truck will run fine unloaded. I can drive it hard and no issues. However, when pulling a trailer (other than the 3 day reprieve after pressure relief replacement), it will pull for about 10-15minutes, then the "whistling" noise, and shut down. Refilling the fuel system (key cycles), and it will repeat the process.
Anyone with additional insight would be greatly appreciated, before I go ahead and replace low and high side pumps, which in Canada are ridiculously priced ($2500 for low side, and about 10k for the high side)
Thank you!