I got a 1988 D100 with a 3.9 V6, I ran it out of gas and now it won't crank. It turns over perfectly fine but it isn't getting gas to the intake. I checked all the lines for clogs and they're all clear. Any ideas???

Also, what exactly is an internal engine control?  

Don't take this the wrong way, but to correct your terminology, your engine cranks but will not fire.  It is a bit irritating when customers use incorrect terminology when trying to describe a problem, so I ask a lot of guestions to get the right information.

Any way, some fuel injection systems don't purge air from the system easily.  I don't work with Dodge and I doubt that they have a schreader valve in the system so you may have to loosen a connection at a fuel rail and cycle the fuel pump until fuel comes out.  *** Be sure to use safety glasses and a wrag over the loosened connection and that nothing will ignite the fuel. ***  If the fuel pump does not cycle (run) with the key in the run position you will have to crank the engine (key in start position).