your filter doesn't have to be below the tank. The outlet needs to be coming out the low place since water settles to the bottom. You just don't want to give the water a chance to settle to the bottom and create rust. Even if you put in a new steel tank unless it is coated you may not fix the problem unless you get the water out.

NOW..Allison problem....
 

Fuel problem fixed ...My allison 6 speed is now locking in gear 4th 3rd and giving a do not shift light....what are the reasons for this an some checks that can be done to find out what the problem may be ..reset it and it throws the light in nuteral ...

Can't really say anything about the Allison specifically, but whenever something like that happens to me the first thing I do is clean and re-seat all the electrical connections.

I had the tank removed and inspected 33ft. pusher winnabago could this have pinched a wire when reinstalled ...and be causeing this ..

If the fuel tank is near the trans harness that could be a possibility or just a connection that has been loosened, go with Nadir's suggestion and check all connectiopns.
What was the final cause of your fuel problem?

My fuel problem was rusty lines to the tank .tank was in good shape just had it cleaned and replaced the pickup and filter .Trans had a lot of debree but i am still thinking wire somewhere..

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Would anyone have the wireing diagram for a allison 6 speed push button auto and if it is possible to bypass the faulty wire from the button to the trans .as a test before tearing apart the wireing harness tank etc..thanks in advance..