Ford Diesel Mechanics help needed

My son's was driving his 2002 F350 Diesel 4x4 pickup truck with the 7.3 engine after getting the transmission over hauled when it just quite running. He tried starting it and it spun over but wouldn't start. The battery light on the dash was blinking. He soon ran both of the battries down and didn't have any lights including dash lights. I pulled him home. Next morning he came out and it started right up and ran fine. Shut it off and tried it again and nothing again, waited a while and it worked just fine again.
Any suggestions on fixing it?
Tom

I'm no diesel mech but I think I'd be looking for a circuit breaker over heating then reseting ???

I looked on ask a mechanic and found several others are having the same or similar problem. Only one suggestion... replace Crank Sensor. That engine was built from 1999 to 2004 and Ford had a recall on the Sensors. Will call our local dealer in the morning. I'll still take suggestions though.

Cam sensor plus also there is a sensor on the front of engine that fills with carbon from a tube that runs back to the exhaust---also--there is an electric boost pump in the fuel system that feeds the high pressure pump--

also if he ran it real low on fuel, he could have air in the system
water in the fuel filter
there is also a fuel related sensor in the top front of left cylinder head

couple more thoughts---the exhaust sensor I mentioned---the tube to it may be plugged while the sensor is still good--you can unplug it by runing a speedometer cable down thru it(rootorutter)

since the trans was out---they could of messed up the wires or fuel lines down by the tank/pump---the booster pump is mounted on the inside of the left frame rail and is easy to get to (makes it easier to mess up working on the trans area) pump is expensive but is cheaper at like Napa than Ford----------

it has been said if you own one carry a crank sensor and a 10mm wrench in the glove box. had a 99 that did the same thing. sold the 99 and went back to my 90 .
fuel maintenance is important with diesels also.

Yep, Cam Position Sensor is a high failure part on these. The IPR, injection pressure regulator, or O-rings on it could be an issue too. If the CPS doesn't fix it, you better put a scanner on it or you're pee-ing in the wind.