Sorry for the stupid question but you did also put the 5.9L ECU in, yes?
There is no good way to actually test the ECU at the dealership, other than to eliminate everything else as a problem, which would then leave the ECU as the most likely suspect. Everytime I've ever replaced an ECU it's always been "I'm 99% sure that's the problem, but cross your fingers just to be sure!" Anyways, the ECU needs to see the crank signal to trigger the coil. Also, there should be B+ at the positive coil terminal when cranking. Double check all your fuses, just to be sure (you never know). Just went out to look at my truck (it's a '96 but is most likely similar) and one large black wire is the alternator output wire. Coming out of the small black "cube" on top of the alternator I have a SLIGHTLY smaller black wire with a white strip which is grounded to a bracket on top of the A/C compressor, along with another smaller black wire. The "cube" I'm referring to has the two small eyelets on the bottom which go over studs on the alternator with two small nuts on them. To be honest, I'm not entirely sure what that cube is. Possibly a floating ground for RFI suppression? Anyways, wouldn't cause no spark. You may also want to double check your crank sensor air gap to the tone ring on the flywheel or flexplate. Should be about the thickness of a matchbook cover away. Easiest way is to take it out and stick a piece of the cover to the sensor, put it back in until it touches and snug the bolts up, or you may have know that already.
