what do you mean one and two aren't sparking? That's not how it works... it's a waste spark system, one side of the coil (with respect to the connector) goes to cylinders one and 4 and the other side to 2 and 3, both coil packs fire at the same time and the same cylinders should be connected to the same sides of the coil packs, the front and rear orientation doesn't matter. There's literally just separate ignition systems that fire at the same time, one on each side of the engine, from '89-94 during cranking only the passenger side fired but once running both fired.
If you have plug wires on the wrong spot on the coil packs that can definitely cause a misfire problem.
If there's an issue with the crank sensor usually they cause a stall when hot but there's more than one way to have an issue. I don't hear of too many issues with the DIS module, I've never had one...