2012 Cruze 1.8 Changed to 2015 1.4T

I have a customer that wrecked the 1.8 in his 2012 Cruze, bought a salvaged 2015 with a 1.4T, Had another shop change the engine and ECU along with the harness from the 2015 into the 2012. Afterwards they couldn't get the car to crank (anti-theft) so they brought it to me. So first off I see that the car originally had an E83 ECU and now with the 1.4T it is using the E78 from the 2015. HPTuners can communicate with the controller, I can see data, and program it etc, but it won't run. I applied the Vats patch to the OS but it will not crank. If I bypass the relay I can crank the engine over as well as command the starter relay via the laptop, but it won't fire.
Heres the question. I have these codes currently

0x7E8: P0315 - Crankshaft Position System Variation Not Learned (Pending, Current, Permanent, History)
0x7E8: P0513 - Incorrect Immobilizer Key (Current, History)
0x7E8: P1631 (Old, History)
0x7E8: P1682 (Permanent)
0x7EB: U0073 - Control Module Communication Bus A Off (Permanent)

And what I'd like to ask is: Is there an issue with the E83 and the E78 and communicating with the rest of the controllers on the network due to the difference in years, that would prevent the engine from running?
Is there a way around this?
Customer is ok with bypassing the starting system and any "quick" means necessary to get the car so that it runs.

No one replied but after updating HPTuners software, I tried flashing the VATS patch again and it worked properly. Car runs great with the exception of what I suspect are bad grounds for the ABS module and the power steering as they don't work. The start circuit also has issues as it will not start with the key but starts perfectly with a bypass relay.