Jumped the starter with a screw driver. The starter works for sure.
OK, so the battery is good enough. You could jump to make sure, but the starter pulls a lot more power than the relays.
So IMHO, it really is test light and wife time. Start with the wire to the starter, have your wife step on the clutch and turn the key, it lights up brightly or doesn't. It likely won't, so you work back in the wiring diagram, each point having your wife do the same thing.
Sometimes, you may find that a wire is broken or crushed somewhere as you test one area but the next doesn't make sense. As Heo said, it may be sensitive enough to show voltage, but a standard bulb would be dim or not light.
In the end, if it worked before you sent the motor off to Jay, either you damaged a wire, left something unhooked, or something failed (like a relay or the aftermarket alarm) all of them are viable, but as much as everyone wants to help, 12.2 to 11.4 really doesn't say much, you eventually have to know the circuit, then just follow it back until you find the cause.
BTW, I would lose that alarm if it is easy to bypass. If you have a chipped keyset it'll keep the crappy thieves away, and the good ones will cut the battery cable and stuff it in a trailer anyway.