Knock Sensor codes (plus more)

Ok some of you may have seen my blown head gasket thread. I got the head gasket fixed apparently, but it seems I've caused several more problems while doing it.

After completing the head gasket and top end rebuild, turned the key and she basically fired right up. Idle was rough, shaking the truck. Sitting in the driver's seat was almost like a massage chair. Seconds after start up, CEL / Trac Off lights up (see pic below for codes).

Ok at that point, both me and my buddy thought the timing must be off by one tooth, cause something ain't right. I take the truck for a short drive, engine seems a little sluggish accelerating and will not shift into 5th gear. So we make plans to rip it apart again and redo the timing..... but after a whole lot of reading about each code... im wondering if timing is actually my problem....

The thing that sticks out to me is SO MANY FAILURES in the system. It's just not possible that all these things were working fine when I parked it, now they show problems.

While reading about knock sensor codes, people say timing issues should NOT cause knock codes, and I see many people have had rodent issues with chewed up wires. I know this is not my case, I was just inside there and have pics to prove it.

How likely is it that my engine wire harness has issues / broken wires now since I was pulling them and securing them up out of the way while working. When I was disassembling the the intake / plenum, fuel rail areas and got to the bulk of the wire harness to unhook. There were parts of it extremely brittle (plastic wire loom cover mainly) and broke off in my fingers without much force at all. I'm really thinking this is the root of my problem now. I'm still going back in and making damn sure the timing is dead on just in case.

So how likely is it that my wire harness is toast (quite literally haha). How do I find out if it is? Any help or insight is appreciated. Thanks!