I finished swapping an M47 into a recently acquired 93 240. I've successfully done this swap on other cars, and this one was routine. Or at least I thought it was.

Now that it's done, when I try to start it it cranks pretty much normally, but doesn't start. There is a bit of hesitation when cranking, though. Here's what I've checked so far:
* Fuel injectors: They have signal, I checked #1 with a noid light while cranking and it blinked as expected.
* Fuel pressure: If I depress the schrader valve on the rail fuel squirts out. That doesn't give me a pressure reading, but there's fuel there for sure, and it squirted out with the expected amount of force.
* Spark: Disconnected wire #1 and grounded it with a spare plug. Seemed to fire just fine while cranking.
* Timing belt: It had been replaced recently, but I took a peek at it through the timing cover, and it looks just fine.

So I'm out of ideas. I seem to have fuel and spark, but the car doesn't start. A few things have crossed my mind, but they don't seem right to me:
* Some how I put the pressure plate on in the wrong orientation, and the CPS is seeing the position of the crank incorrectly. But, isn't there only one way to bolt the flywheel up, otherwise the holes don't line up?
* Damaged the CPS wire somehow (maybe pinched it between the engine and the firewall). But if that was the case I don't think I'd have any spark; either the computer sees the flywheel or it doesn't, right?
* Bumped the CPS when installing the flywheel and damaged it or pushed it too far from the flywheel. But same issue as above, either it sees the flywheel or it doesn't, right?
* Screwed up the wiring somehow. It's a 93, and there are a lot of wires on the old shifter switch. I bypassed the neutral safety switch correctly (the car cranks), and I think the only other wires that matter are the reverse lights, which are connected correctly. Am I forgetting something?

The one thing I don't get is that hesitation while cranking. I can't tell what it is, it's almost as though for a split second the car fires against the rotation of the starter.

Any thoughts? I'm hoping I'm overlooking something boneheaded, like I often do. I can't for my life figure out how I seem to have spark and fuel, but it won't start.

Thanks as usual for all the help!