The sticker I was looking for is an over-ride sticker for the key... given the age it was a bit of a long shot still being there, but was worth a check. It stands out pretty well, has a small barcode then two numbers one an MR###### ***** other an A######.
If it were there, we could temporarily bypass the immobilizer.
At this point unless there is something additional to add about what transpired during the transmission swap, I don't see any expectation here other than an immobilizer malfunction.
Since you aren't 100% sure the engine light worked before, I would take one last check over the fuses just to be safe. It is unlikely an issue (and more probable the light was burned out before) since you have consistent spark, but doesn't hurt to re-check.
With constant/consistent spark we know there is a good crank sensor signal, and your compression is at least adequate to run. That leaves us only with a fuel related issue to suspect.
At a fuel related issue you have a few possibilities.... of course fuel itself, pump/pressure, as well as cam sensor and immobilizer. We checked the fuel injector pulse and right off the bat see that there is no pulse.... so fuel itself and pump/pressure are pretty much out the window. That leaves us with cam sensor and immobilizer.... and if it were the cam sensor we would get momentary pulse then nothing (not to mention they rarely fail unless aftermarket). With no pulse whatsoever, that really only leaves us with immobilizer or computer issue.
What I would be doing at this point is getting it into a dealer so they can confirm computer operation while they are there, and then reprogramming the key and seeing if things change. That injector pulse had to go somewhere, and unless the harness go downright mutilated somehow (which would be quite a task given the distance from where you were working), we really only have the computers and immobilizer to consider, and the immobilizer (keys specifically) is the only one that is pretty common to randomly fail.