Wow that is awesome!!! Thank you so much for doing all of that. I think I can get it figured out now.

The only other issue I have left is that knock sensor. I checked the connection there and everything looked snug.

Where does that multi plug wire run from the knock sensor? I remember a really thin black wire that ran behind the auxuliary housing. Is that the one?

 

I'm not positive. It runs back into a large section of loom near the fuel injectors if I recall. I know you should be able to see it come from the sensor up around the left side of the driver's side head as seen from the front of the motor (behind the PAS pump and AC compressor, etc). If it's still connected through there, I'd suggest trying to see if it's scarred up anywhere along the way. I was suggesting that you may have clipped it/crimped it/etc as you put the driver's side head back on, so check near where the head connects to the block in particular.....I'd suspect if you got it anywhere, that would be the place.

If that doesn't help, I'll try to get some pictures of the routing from the motor I have out tomorrow for you.

 

I just pulled off the auxilliary housing and I had the knock sensor wire pinched in there pretty good. Flattened to be exact. Is it possible to replace that wire?

 

Hrmmm....that's another one I'm not sure of. As I mentioned, I've parched one before with good result, so I suppose that means you can get one from a junk harness and patch it in above your problems area, but I don't know if there a better way of approaching it (like if it has a connector somewhere close in the wiring harness.

I'll have a look this evening for you and see how far I can trace it back. I'm sure it will be a whole lot easier with the intake manifold off.

 

So I've taken a look at the knock sensor wires. Unfortunately, they follow the main harness all the way back to the ECU (through the firewall on the passenger's side). It is coax all the way through, unbroken.

As I mentioned, I have patched one of these before. Maybe you can find the break and repair it, or clip a good section out of a harness at a salvage yard and patch it into your harness before the damaged section. As with any coax, try to keep the section of the outer conductor that you have to unbraid as short as possible. I soldered the center conductors back together, taped over the joint, soldered the outer conductors together, and put some heat shrink tubing over the entire repair followed by some more tape. This repair was done on a friend's truck, and its still going over a year and 20k+ miles later as far as I know.