Have a load test done on the batter to check for failing cells. For diesels to start any thing less than a fully charged battery good battery is a waste of time as the engine needs fast RPM to heat the air to ignite the fuel and slow rpm's just doesn't cut it.
SOURCE: 2002 7.3 F350 WONT START
starter might be going bad that can cause it to drain the batterys
did you check to see if it is getting fuel if it has duel tanks the valve to switch tanks can go out and that can stick in a position were it doesnt allow any fuel to pass it could be the pump too
SOURCE: '03 F-350 7.3 Powerstroke cranks but doesn't start.
with out doing alot of testing
we have found alot of cam sensors going bad in the 7.3 powerstrokes
i just had one in last week with a new sensor that only lasted a month
SOURCE: ford f250 superduty turbo diesel 7.3L Will not crank
Charge the batteries. take a Reading to make sure that you are getting almost 14v to both batteries. If it is not charging then take the alternator back off and have them check it. you might have bought a bad one. There is a way to test the glow plus with out taking them out. ( Take a piece of wire long enough to reach all the glow plugs from the battery. unplug the glow plug wire.If you touch the end of the glow plug with the hot wire it should make a little spark. if no spark then the glow plug is bad. do this to each one, but one at a time)
SOURCE: Ford 350 diesel truck batteries draining.
ALL FORDS DO THIS/ JUST RUN IT FOR 15 MIN ONCE A WEEK OR TRADE IT IN FOR A DODGE
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These engine need to crank over fast to start. First thing you should have the batteries checked. Next check the cables and then the starter.
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