I deleted the water seperator on my jetta as well and installed new lines from tank to the engine bay. Your problem reminds me of my old f250 which I need to fix. It had these plastic senders that broke off and took the bottom 1/4 of the tank away and let chunks get sucked up into the fuel pickup.
Don't know if our systems are the same but I have had the whole unit out of the tank in my jetta. It goes from the metal lines sticking out which are fused into a big plastic casing and the bottom of this has a little plastic grill type deal that I guess catches chunks. When I got my neglected car home last year I took it out to clean it, it had debris for sure, but it wasn't clogged. Looked like a little mud was smeared on it.
Anything is possible I suppose but I wonder how that unit would get cracked at the metal lines. Perhaps plug it if you can and run low pressure shop air under water and check for pinhole leaks. I don't remember if you can actually get to the end of the metal tubes that sit at the bottom though.
If yours was good like mine, I would guess maybe there are other issues with your filter, pinhole in fuel lines or air vent clogging?
On mine I have actually driven on freeway and up/down mountain pass with it down at the bottom of the red just for a fun test with some extra fuel in the back
I wanted to test it to see if I could last going over a pass of 20 miles with no gas station.
I never did measure the actual fuel left at the bottom of the red either, just tried that test a few times. And I actually have never had that rough, running out of fuel condition like on my truck from sucking my tank that low which I do pretty frequently, way under 1/4 tank.
Another though and I am not sure on this, what is the effect on the gauge vs. the actual fuel level if your sending unit/pickup wasn't orientated arrow to arrow? Possible its positioned wrong and your fuel is lower than you think?