I have a 2003 f250, straight exhaust, 3.5 in down pipe, super chip programmer turner on high, afe brute force 2 air intake, and an unplugged egr valve. I just replaced my batteries about 3 months ago so both batteries are new. hooked up some cables to it and slapped em together and sparks flew everywhere so the batteries seem hot. I get in to crank it up and it acts like the batteries are dead starter clicking and gauges jumping. I hook up another car to it to jump it off and it will crank after it has set there for a few minutes. let it run for about 2 hours and kill it, same thing happens. I have the alternator off right now about to get it tested today. let me know what you think.

 

what about your starter or wiring and you said your getting your alternator checked

 

would say it could be the egr but with it unplugged i have no clue...
alternator/starter/wiring for both

have you tried removing the superchip

 

are the battery terminals and wires clean, corrosion free and tight?

 

took alternator to autozone and got it tested. it was shot. bought a new one put it on jump her off and shes back running again. thanks for all the help, i thought i was probably the alternator that why i tried it first but i was starting to think worst case scenerio's