Engine swap Trouble codes

About one year ago I bought a 2012 prius with a blown head gasket and swapped that engine out for a JDM engine (see here) and after diagnosing running rough as counterfeit plugs it has been running great.

2 weeks ago I bought a 2011 prius, this time with legit holes in the engine due to a head gasket failure followed by hydro lock in cylinder #1. I got another JDM engine and looked it over inside and out. To me the cylinders seemed to have very little carbon, and the oil I drained out was in good condition. The EGR cooler was still really clean (could see light through it) so I went ahead and dropped it in yesterday.

I finished hooking everything up this morning, and just pressed the start button. The engine ran really smoothly for the first few seconds, but then got very rough. The car said "check hybrid system" and "oil maintenance soon".

When I scan it I get several codes:

Permanent:
P3190 Poor Engine Power
P3191 Engine does not start

Others:
U0073 Control Communication with Bus "A" Off
U0123 Lost Communication with Yaw Rate sensor Module
U0124 Lost Communication with Lateral Acceleration Sensor Module
U0126 Lost Communication with Steering Angle Sensor Module
U0293 Lost Communication with Hybrid/EV Powertrain Control Module

When I bought the car it had the p3190 already. I did not scan all the modules, so it could have had the U0XXX ones as well.

I of course am wondering "Did I plug everything back in?" I did take my time with hooking things up, and I have done this once before. From the top of the engine I can't see anything that is disconnected. I am using the plugs, coils, and injectors from the JDM engine. The condition of the plugs looked fine to me, and they looked legit, but I of course have been fooled before. I DID put oil in the engine, something that I somehow forgot to do on the one last year and quickly realized my mistake. If the oil pump did not work it would say "low oil pressure" right?

The communication codes make me think that there is some kind of ECU or electrical issue. This did sit for about 9 months before I bought it. I just put in a new 12V battery

 

Ok, so I tested the 12V voltage, 12.6 so that's fine. I disconnected it for an hour or so. I started it again, ran rough. I thought that maybe something was up with the EGR valve, so I did the putty knife trick. Started again, ran rough....for like 15sec and then started to even out and became pretty smooth. Turned off and on and this time no real issues! I took the putty knife out and still ran fine, even turning off and on. I ran in maintenance mode for about 10min without a problem. YAY! I think the putty knife was a red herring, and that some other part of the car needed to be reset/get used to an engine without literal holes in it. Fingers crossed for a smooth sail from here! I do wonder if those communication codes will resurface, and then I will be back for thoughts!