Not silly at all. I think it's going to be a case now of doing exactly that - going over each and every sensor, making sure it's plugged in, and plugged in to the right connector on the harness. Fortunately MSD made it so easy to check.

Now that the ISCV has been changed with new, literally the only remaining original sensor is the TPS, everything else (crank, phase, ect, knock, oil pressure, act, etc) was replaced with new when building the engine up.

One thing I haven't got connected up yet is the diagnostic LED breakout from the MSD loom. I've got a dash warning light and a toggle switch ready for that. I guess it won't hurt to see if the ecu thinks there are sensor problems.