Several months ago I removed my rear tank to get a leak fixed. Before installation I cleaned the inside of the tank and put a "bed lining" on the outside. While the tank was out I noticed an occasional spitter/sputter and loss of power. I thought I had a lift pump going and replaced it, it didn't solve the problem. Now with the rear tank back in, the front tank runs fine, but the rear tank doesn't. Since the first fill up on the rear tank (filled the front tank at the same time), the spitter/sputter is happening on the rear tank. My yellow fuel filter light comes on (never knew I had a light there) during the loss of power episode. If I switch to the front tank it clears up (both light and sputtering) in a mile or so. I have changed the fuel filter several times.
Unless somebody points me in a different direction, I think it is the tank switching valve along the frame rail.
My theory: With only the front tank installed, the valve was allowing air to be sucked into the fuel system, thru the open rear fuel line, causing the spitter. With both tanks installed and sucking off of the rear tank, the valve is not fully opening thus causing a restriction in the line (low power + fuel filter light). Running off of the front tank with the rear tank installed - closes the fuel system so if it tried to suck air it is pulling some fuel (5%) from the rear tank. Does this theory make sense?
Could it be something else??

 

Check the lines to the rear tank, maybe something got squished when you strapped the tank in.

 

Also look for cracks in the lines and all the connections . If all the lines are good you can pull the valve, drill out 4 small rivets, inspect it, put it back together with screws.

 

External lines are OK, there could be an issue with them internal to the rear tank. Are the valves the same for gassers as for diesels? I have 2 gassers for parts that I can rob parts from.

What is the criteria for turning the dash fuel filter light on??

 

Gasser valves are different, pretty sure they can't be used.

The dash fuel filter light is controlled by a vacuum sensor in the fuel filter mount. When my lift pump was failing it would come on if I was flooring it while accelerating, or the highway (pedal also floored). At first I thought it was the filter, then the lift pump crapped out completely and left me at the side of the road. However, I was only running one tank at the time.

Since you only have problems with the rear tank, its either the valve or the tank. You probably need to disconnect the lines at the valve and see if you can suck fuel out of the tank (or blow air back through) and see what happens. If you have no problem, then it could be an issue with the valve itself.
Oh, visually looking at the lines may not show an issue, but there could be something inside plugging it up.