I wouldn't be surprised if your system voltage dropped to 9V while cranking. A starter draws a ton of current! That said, 9V should be sufficient to get you up and running regardless. The entire system runs on a 5V reference architecture and should technically run on anything more than 5V of supply potential.
If I had to guess, I'd go with a poor power or ground connection somewhere. I'd start with checking every single connector that has a power or ground going to it to make sure everything is good. From there I'd be checking point to point on the harness from every engine side connector to the PCM. If that pans out, you really need to get yourself access to a Tech 2 or MDI so you can check your cam / crank sensor counts while the engine is turning over to verify if you've got signals from the both of them as well to verify a believable reading on the rest of the engine sensors. You require both the cam and crank sensors operating correctly for the PCM to know where it is in the timing cycle and to fire the coil packs accordingly.
If you don't mind a couple weeks wait for shipping, I'd be happy to do the point to point wiring check on your harness for you. Your connections to your truck should be pretty straight forward and the heavy gauge pink wire that ran to your old ignition coil is perfect for the ignition input to your PCM.