Help ?!?!? Fuel Issues ???

96 7.3 f350 , The truck sat for a couple months while i painted it . with 3 mostly full tanks . After painting , i topped off tanks and started driving to work , after a week or so the fuel filter light came on and the water in fuel light . Drained off the bowl and put new filter in . But the filter light continued to come on from time to time until one day coming home from work it quit . Towed it home , and the next morning it started up no problem . added power sevice 911 to tanks and drove around the block a few times , filter light came on , so i changed filter again , with no luck . a few freinds told me the fuel pump / lift pump was gone so i replaced it and cleaned regulator. awesome , great , runs better than ever . then the fuel filter light started coming on again under load . researched and thought maybe a bio problem so i added power service bio kleen , and drove some more . also gauges dont seem to be reading correctly now , so after a week or so , ( light still coming on but running great ) i topped fuel off . My aux tank was almost empty which is the one i think i have been running on most of this time . But my factory tanks seemed to be pretty much full only took maybe 5 gal between the 2 tanks to fill . Drove for a few more days and i thought i should try the other tanks . When i did filter light came on immediatlely , and shortly after started sputtering . So i switched back to aux tank . Later i tried the other tank with the same results . SO i get it home and figure ok ... the light doesnt come on with the truck at idle so ill let it sit and run on the stock tanks and get that old fuel out . I did ... and went inside .... about 30 minutes later the truck dies . Wont start , so i switch back to aux tank , no luck she still wont start , i have blown the lines out from fron to back and back to front . Chargin my batteries back up now or i would still be out there screwing with it . ANy ideas ?