My son says his truck won't start with the key but will when hotwired. Possible problems?

you stated pump kicks on put clutch in and no start so what would you hot wire [[and dont hotwire anything ]]]which causes more problems and in this case is probably pump not problem ----theirs a clutch safety to start in manual trans which that or ignition system problem such as failed starter --ignition switch --etc have vehicle for any possible trouble codes

No. it wouldn't keep it from starting. If the engine cranks but won't start, probably gas or spark (ignition) related. Do you hear the fuel pump in the tank turn on for a couple of seconds, when turning key to on, not start? If you cannot hear the pump, better check if you are getting gas up to the engine. Maybe the fuel pump quit, or the pump circuit needs looked at. The pump should briefly turn on with key on to pressurize the fuel system-the fuel line and the fuel rail where the injectors are. Then the pump will turn off, and only come back on again when the engine is cranking, and stay on when running.
Correct fuel pressure is important for easy starting, and good engine performance. Have the fuel pressure checked against the specification for your vehicle. If fuel pressure is good, check the ignition system-check for spark.

listen fore the fuel pump when at each stage of the key turn.
Its one of the least thought of problems the fuel pump.

You need tune up,cap or coils,could be crankshaft sensor,camshaft sensor,maybe fuel filter.

possible

To review - - the fuel pump in the tank pumps fuel to the injectors.
There is a fuel shut-off which works in a wreck to prevent a fire.
If the plunger is down, the switch is on. Normal.

It is possible the fuel lines are full of air which would take a long time to purge by cranking the engine. Sometimes you have to use starting fluid or other means to "run" the engine long enough to get gas back into the injectors.
As long as the engine cranks, the battery is fine.
It is also possible the pump was damaged when the tank was run empty. The pump uses liquid fuel to cool and lubricate the electric pump. It can overheat when running the tank below 1/4 full.
It is also possible the fuel filter was clogged with junk from the bottom of the tank.
I would get someone to check for fuel pressure at the injectors and try some carb cleaner or starting fluid in the intake hose next.

It sure could be. But, first...by "won't turn over" you do mean it cranks at normal speed but won't start?
A simple test of the fuel pump is to stand by tank and listen as someone turns key to on. When first turned to on, your pump will activate for 2 or 3 seconds, pressurizing the fuel system, and then shut off if the engine computer doesn't get a cranking signal. Do you hear it come on? If not, then something's not turning your pump on. If you can hear it buzz on briefly, then maybe it's your filter. Another test: Spray a little starting fluid into your intake manifold (remove the big hose going into intake manifold) while someone tries starting it.If it doesn't fire and try to stay running, then it's probably an ignition problem. But if it does fire off, then you know it's a fuel problem-likely your pump or filter. good luck.

it all sounds good, i would lean towards the distributor as since it warms up it runs fine. Hope this helped Tim

possible fuel pump check by spraying throttle-body cleaner in the intake hose while someone cranks the car

I am having some issues with the fuel pump we suspect. The fuel pump is located in the fuel tank and occationally I can hear a motor running secondary to starting the diesel. As things have progessed i initial thought perhaps I had a hole in my muffler, but my mechanic has assured me that is not the case. The fuel pump may be a good place to start.