When I turn the key there is nothing, no crank, no start, no fuel pump?

Hello, we have a pinout for the PCM for you, have you gone through with a test light and verified all the fuses have power? And does the Check engine light come on at key on?

The 1st diagram is the oem PCM powers and grounds. Diagrams 2 and 3 are top and bottom page one of the entire PCM wiring diagrams, 4, 5 page two, 5, 6 page three, and 7, 8 page four top and bottom.

You have power to both wires at the starter with the key in start? And still no crank? If so, put a test light on battery negative and touch the engine block, if the test light lights up you have no ground to the engine block. Here's the starter wiring diagram.

I would go through and verify all grounds again, you didn't swap out PCMs or anything correct? Just an engine swap?

Yes, but even if the grounds are in the proper locations, which doesn't mean they can carry current, if a ground wire is bolted to a location that has paint on it, or the ground eyelet is not good, you will get strange symptoms like this. If there is power to both wires on the starter and the starter solenoid is not clicking to engage the starter motor, it sounds like you are missing an engine ground. A test light hooked to battery negative, then touching the engine block will tell you if the block lacks a ground. Because power is already at the starter, providing a ground with a test light to the engine block will light it up.

Or you can try just hooking some jumper cables from battery negative to the block and to the body, providing a temporary ground, if it comes to life, you know what the issue is.
Does this new engine even turn over by hand?

Well, with power on both starter wires, if it's a full 12volts, and the starter is not engaging, either your starter is bad, or there is no ground. A bad starter will usually click the starter solenoid, but not engage to the flywheel, you wouldn't have power on the ignition switch wire at the starter if it was the Immobilizer security issue, the PCM would not energize the THFT 1 or 2 relays. I will have to continue with this tomorrow, its already midnight here.

What voltage reading do you get on the solenoid wire (trigger wire) when attempting to crank it over?
I would also do a voltage drop test on that wire from battery positive to the trigger wire and see if there is some huge voltage drop occurring while trying to crank. Jumping to the solenoid from the heavy gauge starter wire obviously doesn't have any voltage drop on it and it's provides enough current flow, so there might be an issue where the trigger wire can't carry current.
If you read high voltage during cranking, that's the amount being lost on that wire due to a connection issue somewhere. Do that test first, you might need to have someone else crank it for you so you can monitor the multimeter.

Okay, there's got to be something going on with that wire from the ignition switch, you could be reading 12volts on that wire, but it just can't carry any current flow. A voltage drop test should reveal that. I assume you were measuring the voltage on that wire with it unplugged from the starter? And it read 12v with the ignition switch cranking?