So I left the shield connected to the negative VR wire with the 10k pot inline.
I then soldered in line a 10k resistor on the TachIn line going to the positive VR.
This actually caused my RPM threshold to drop from 4k to 3k. So I then put the shield back onto a ground line, and my threshold raised back to 4k. Although slightly less than the 4050 I saw last night.
So really the resistor didn't do much if anything. So I decided to try swapping the TachIn input to the negative VR signal before giving up until I can get a hold of an oscilloscope, and voila it works perfectly.
Can take it all the way to redline now without a problem. It was pretty jerky though until I turned off the Tooth Logger, so that was fortunately just a bandwidth issue.
Thanks for the suggestions, and now in case any of you guys somehow end up with a VR crank sensor, you'll know to use the negative.
I am not sure if the 10k resistor on the TachIn would have been necessary or not. It doesn't hurt, so I am just going to leave it in, since unsoldering it would be a pain.
The shield really doesn't seem to matter at all. I left it dangling and it didn't have an affect. I am going to leave it on the ground wire since that seems to make the most sense to me. Clearly the 10k pot is unnecessary but I'll just leave it in too I guess.
Here's a snapshot of the noisy signal I got with the negative side.
But now that I think about it, the wiring diagram for the car doesn't specifically say which wire is positive and which is negative. They are both AC signals just inverted from each other from my understanding, so it shouldn't matter.
I just followed the install guides and labeled pin 21 as positive and pin 22 as negative, it could very well be the other way around. There's no way to really tell.
Ok that's enough from me.