Hi,
Wow, that's a lot. Here is what I need you to try: Reconnect everything but the air intake temperature sensor (AIT). Clear the codes and see if it runs better and if the codes return.
I attached a pic of it below to help locate it. I'm suggesting this because you have a misfire issue. Yes, the CKP could cause that, but the CKP wouldn't set the AIT code. If the AIT is bad, it can cause a misfire.
Let me know what you find or if you have other questions.
Take care,
Joe
See pic below.
Image (Click to make bigger)
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Tuesday, February 8th, 2022 AT 8:26 PM