Yeah the van was the biggest plot hole. It was a 2nd gen Plymouth Voyager which came out in 1992 and all of its available engines were fuel injected.

First the EMP happens, then as Tom Cruise walks by the shop, the van is already getting worked on. Why would the mechanic guy already be working on a car that had just been fried by the emp? How did the person that owned the car get an appointment so fast? And the engine computer is what would be fried, not the starter.

So as Tom Cruise walks buy, the mechanic says to him, "man the starter's fried" and Tom tells him to "replace the solenoid." So then a bit later when they steal the van, it magically works because the mechanic guy replaced the solenoid even though it shouldn't work because the engine computer is still fried from the EMP.

Even if the car had already been in the shop to have its starter fixed and the mechanic guy was workin on the starter as the EMP happened, the engine computer still would have been fried and the car wouldn't have worked.

As for them not filling it up with gas, it could have had a full tank. It's not that long a drive from New York to Boston and they didn't even make it that far with the van.

Now on the other hand what they should have done was take Tom Cruise's Mustang that was shown in the beginning, because it obviously had no engine computer for the EMP to fry.