Electrical SKS Woes

I have been trying to sort out all of this on my own and I've spent a lot of time going through all of the wiring diagrams that I have and threads on here, but I can't seem to sort out the issues I am having. I am really hoping it is something dumb but here we go.

My car is an 05 but I swapped in an entire harness from a donor 07 as I wanted to have the smart key function. Everything worked properly on the 07 so I am trying to sort out what has changed. I assume the issues are related but I'm having a couple different problems.

1) the SKS start (key in the car and not in the slot) does not work but the proximity unlock and lock seem to work except for the rear hatch. Everything powers up fine with the key in the slot.
2) the rear hatch does not unlock/open with the handle switch but it will lock the car if I click the black lock button.
3) checking all the communication with the oscillators on my scanner it looks like everything but the outside one behind the bumper is having an issue. The two pictures are the error codes I get from my scanner. The first, #33, is when I go to check communication with the interior rear sensor. It beeps and confirms communication like the rest of them until I back out but it does give this error. the #36 error code comes up immediately when I try to test the outside sensor (the one under the bumper) and there is no confirmation beeps. I checked all the connections, continuity wise anyways, at the oscillator, antenna, and up at the ID2 connector at the driver door. The connections all seem good and it is receiving power and ground. Now, I haven't checked from ID2 to the certification ECU, but plan to tonight. I don't know if the error codes that my scanner gives me are even useable so my next assumption was that I was going to have to get a techstream.
4) when I go and unlock the car with the touch sensor (driver and passenger), it unlocks and beeps a ton of times instead of the normal 2. I found this thread Actuators and Blinkers Go Off When Door is Unlocked Keylessly | PriusChat and it seems like mine is doing something similar, but I didn't see what the eventual issue ended up being.

I have also confirmed function of the SKS button under the steering wheel as I know that is sometimes the cause. I also put a brand new battery in the fob and I am 100% sure the 12v battery is good.

I am thinking everything is related but I'm not 100% sure. Any help is greatly appreciated. I have a few other electrical gremlins unrelated to the SKS but I need to do some more searching first to see if I can figure it out.

 

I forgot to mention that I took both of the front door harnesses and swapped them. I swapped the hatch harness as well.

 

That is what I assumed they were but I wanted to double check. My scanner has a separate section dedicated to the Smart Key System so that is where I was doing the tests.

I discussed a good bit with Tombukt2 and looked into a few things but still couldn't sort it out. I ended up downloading Techstream and trying to diagnose it that way but again had no luck. The odd thing though is that my trunk door unlock switch started working again. I noticed looking through the data on Techstream that the latch was somehow stuck in a "prevent" mode for allowing it to open. I did one of the calibration updates for the system that Techstream allows and it seems to be working now. It still does not see the key outside of the car in the back but if I hit unlock then the hatch release switch will actually work. It still does not recognize the key inside the car though to be able to power everything on without the key in the slot.

In Techstream it shows that it cannot fully communicate with the SKS computer though so I am not sure what is going on there. I do have some main modules unplugged that I am not using as the entire drivetrain is different so I will have to recheck some of the communication lines and see if they run thought some of those modules I am not using. I might just plug them all in and see if it makes a difference too.