I'd never go down to 1/8 tank on an older truck. Any rust or moisture from condensation will get sucked into the fuel lines, and the pump is cooled by the gas in the tank so it runs hot on a low tank and shortens it's remaining life.
Common misconception. I've explained why more than a few times over the years. As someone who used to build the tanks for these trucks, trust me, it's not possible. First, if the gunk is in the tank, it doesn't matter how low the level is. The reservoir the pump sits in will stop that from happening. Second, If it happens to make it into the reservoir, 99% of it is going to get stopped by the sock or pre-filter on the pump's sending unit. Anything that makes it through the sock isn't going to hurt the pump. Anything that makes it through the pump isn't going to make it past the fuel filter, and anything that does make it past the fuel filter isn't going to hurt the injectors.
"But what about the heat?? The low level lets the pump get hot, and everybody knows heat kills pumps!" The return line from the fuel pump dumps into the reservoir. So long as there is enough fuel to run the motor, the return line is bathing the pump in fuel.
Anecdotally-speaking, I've got 175K on mine, and regularly run it until the light comes on and then some (been out of gas on the side of the road three times, and had it sputtering to limp it to a station two other times). Still the original pump.
{/hijack}
Seems by far the most common misfire is #4 with the 4 liter. I had to change #4 plug on my 99, then all was swell. I don't know why it went bad. Sorry, don't have any help for fuel problem. Good luck and please report the fix when you find it. Inquiring minds you know.
Just thinking out loud, don't cylinder 1 and cylinder 4 share a coil pack? I'm wondering if one of the wires cooked through? Or one of those two plugs took a dive? Coincident with the fill-up....
I doubt it's the fuel... If it was that much water that it pumped the tank full, it's not going to show up as a mis-fire on just two specific cylinders. That same fuel is pumped to all six...