I got out and messed with it today.. still not right!

I will run fine off a container of diesel but when I try to run it off the tank it has problems. So I figured that my diesel fuel was bad.. sucked it all out of the tank and replaced it with 5 gallons of fresh new diesel. I also removed the rubber lines from the engine and tank side and blew compressed air threw the lines. Hooked it all back up and nothing... I used my vac pump and could only draw fuel from the return side under the hood. This told me I got the lines under the tank backwards... got those switched around and it now runs off the tank.

Not so fast batman..
When running the primary filter fills with fuel then empties then fills again then empties... it's a cycle of filling and emptying. The engine gets really rough and shakes bad during one of these cycles. It seems to me the engine starves for fuel then smoothes out once it get's it.

So whats the deal? Could the lift pump actually be bad? Perhaps it will suck fuel from a remote container under the hood but not from the tank? The tank screen really looked fine when I pulled it. Maybe the tank is clogged in or about the tank screen? When I swapped the lines under the tank fuel poured out of the bottom port just fine.

Any ideas? The car just turned 300k last summer. Time for a new IP?

__________________
08 R320 CDI current

Past
95 E420
87 300D Turbo 5spd
90 300TE
83 300SD
85 300TD
92 400E
85 190D