Take multiple pics of how you are set up. I might be able to offer suggestions. Besides having had a ase master cert in truck equipment (amongst others) I was partners in owning a truck equipment shop.
How you fuel a dump is a common place of error. We used to fix the issue for many companies that had the truck built at our competitors because it was cheaper up front price. By the time they learn they have a $40,000-$100,000 paperweight, they brought it to us and spent way more than they would have doing it right the first time.
In Nv and many other states it is legal to raise a bed and use safety support in order to fill the tank(s). The labor and nuisance is often the choice over custom tank or bed modifications required.
Has someone modified one or both of the factory tanks? Their base design was good, never had issues with the tanks themselves until many years later and the introduction of ethanol/methanol into the fuel which delaminates the coating inside the tanks over time. For the solution to that, stripping the interior of the tank or simply new tanks to replace them, eliminating the internal screen (aka sock) and using a pre filter exterior of the tank. As it sounds you have already learned a quality aftermarket water separation systemis a worth while investment. While doing all that upgrades to the final filter and lift pump make sense since they are poor to moderate at best. The Airdogg and Fass both come across as good options. You do need to modify tank inlets for them both and new lines. External fuel pressure gauge tapped at the ip is a must but pays for itself even in stock setup so that is a no brainer.
Modified tank access is no biggie compared to new tanks. New tanks obviously mean built to handle the additional lines and larger sizes. If you choose custom new tanks, using the old ones as a beginning pattern saves a lot of time often.
There is not many, or any that I know of, custom mass made tanks for these trucks because the factory ones are so low cost to replace. Rock auto has stainless steel ones for $300. Custom build stainless is going to cost $1000 in any shop, maybe more depending where you are. So replacement is where to start usually. Custom out of mild steel is around $600. But then you need to coat the interior...so square one in a few years possibly.
Not trying to sound like a jerk, but if you were a certified welder and fabricator you wouldn’t even ask. So understand to LEGALLY build a fuel tank for on road use in the USA you have to hold an ‘R’ stamp certificate, not just 6G or 6 position. So other than backyard bobby, you aren’t going to be paying some cheap hourly rate.
In real world not court room, Any decent fabricator can build a descent custom tank. Be leary because many get the ‘solution’ of tank outside the frame rail or other dangerous ideas. And since your truck isn’t tested for it, you become liable more than the welder/fabricator. Even when you sell the truck and the next owner has it- since you commissioned it.