questions about fuel lines going to selector valve/ air getting into system?
 

ok so I have air getting into my fuel system before the water separator. I was planning on just replacing ll the fuel lines from the tanks all the way to the lift pump and to the fuel filter.

I started looking at all the fuel lines. and there is 4 lines going into the selector valve. two from each tank a big one and small one.

what do both lines do? is one a return line or something?

yes, there is a return line. the supply and return are both switched by the selector valve.

if air is getting into your system equally on both tanks, then its likely that the problem is either in the TSV or in the water seperator, or in the lines between them.
if on the other hand, it happens primarily on one tank or the other, then look for a problem between the offending tank and the TSV.

the small (5/16) lines are return, and the large (3/8) lines are supply.

I have the water separator bypassed right now. I have some 3/8s clear hose attached with a barbed union to the hose going into the water separator running into a 12v inline fuel pump then going to the fuel filter.

originally when I started figuring out the air issue it seemed to run just as rough on either tank. after bypassing the lift pump and installing the clear tube I have noticed a lot more air bubbles in the line when I switch it the rear tank.

when I run it off the front tank I still notice some air bubbles but they are far less and much smaller.

try running a piece of clear hose from one of the inlets of the TSV into a can of clean diesel, and running the truck on that, that'll isolate problems in the TSV from those in the lines or pickup unit in the tank.

FWIW, there are a number of people here who have had problems with the pickup unit in the tanks rusting out, causing leaks

Also: Put a check valve or squeeze-bulb(which has two) in your input fuel line, just before the water separator or injection pump. It solved /all/ of my air-intrusion starting problems, even when I *know* the return lines are leaking(even with one return line broken and open to the air, it still didn't drain down).

how does a check valve stop air from getting into the fuel system? wouldn't the air go past the check valve into the injection pump?

If the air is getting into the system in the fuel tank pickup, yes. If it's the far more common issue of air getting in the return line system somewhere, it'll solve that problem entirely.
It might even help in the former case if it runs at all, as you'll likely not have any drain-back issues, even with a little air in the system.
What I do know is that it's a very simple solution which seems to solve all manner of small issues, and which allows you to manually move fuel through the system if you get stuck.

As far as your selector valve goes, you should have a return line to each tank as well as a supply line, and then two lines going up to the engine.