It really hurts your truck to run it out of diesel fuel. But if you do find the need to do so, lets take these steps every time this happens. 1st always keep about a 1 galon gas can full of diesel fuel if you like doing this often. Your truck has a large fuel filter that looks like a really big oil filter near the intake lines to the intake manifold. when you fun the fuel dry, this huge filter becomes empty and until it is compleatly full again, all your engine will do is suck air. If there is any air what so ever in this filter the engine will take a while to start running again and with deal damage to the engine. first take off the filter, fill the filter half full of diesel and swish it around a little, continue filling the filter until it over flows. being careful not to spill anymore, screw the filter back into place. And don't let it happen again, you'll thank me when you don't have to replace that 9 thousand dollar engine of yours.
Your situation is called an airlock, as expected a diesel engine will not run on air. If there is air anywhere in your fuel system it will be difficult or impossible to start the engine. There are different procedures for different engines. Read your manual. A generalized procedure is to fill the tank with fuel, fill your fuel filter if possible. Crank the engine, some engines have an air bleeder, and some you will have to crack an injector line to let air escape (you should see some fuel weep out). Once you get a cylinder firing let the engine run until it smooths out.
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Since a diesel will keep running until the fuel is shut off ( no spark necessary ) it goes to reason that it will not run until the fuel is turned on.
Most diesels use a fuel relay and a fuel solenoid to turn the fuel on and off, during the start cycle a current is sent to the solenoid to pull ( open ), once the engine has started a lower hold current is then applied and the pull is stopped.
Check the relay first since the solenoid is operational at least in the pull mode, if no luck there move on to the solenoid. There is the offhand chance that it also might be an ignition switch problem but it is far less likely.
It could be the keyswitch or the starter could be wired wrong.
There is a chance of it, that engine has glow plugs, starting fluid can explode when the glow plugs come on causing engine damage. Before using starting fluid on this type engine, make sure glow plugs are not plugged in, and can not come on.
Just because you hear the pump come on doesn't mean it's pumping. Or that the fuel line is hooked up just the way it needs to be. You'll need to pull the pump again and check it to be sure it works. Don't rule out an inline electric fuel pump somewhere between the tank and engine. It got my Chev. truck running again with very little hassle.
The check engine light can come on for literally thousands of reasons. If the truck is still running well, odds are it's nothing too serious. See related links for a free article I wrote that explains in more detail.
Change the fuel filter. Also, if tend to wait for the empty light to come on you're hurting your fuel pump. Hence, the jerkiness