The speed sensor generates 4 pulses (in mediocre waveform) with each revolution, and the signal is further refined (squared up for better digital signals) to use to determine vehicle speed and therefore shift points by the ecu.
Does the speedo read normal and smooth? Or does it jump around? If nice and smooth as you would expect, I wonder if you'd also look at the bank 1 oxygen sensor and connection below that. Also check vacuum hoses nearby in case the sprayer knocked one loose.
IIRC there really isn't a whole lot as far as wire harness and vacuum lines down by the steering rack. I mean MAF and other wires are on top of the valve cover back there.
You can try reading off fuel trim numbers. Or even just disconnect that oxygen sensor connector and pull the 15 amp blue EFI fuse to reset the fuel trims in memory back to 0. Do an idle engine test and/or a short test drive (while in open-loop mode), and see if you still have that hesitation. You'll get all kinds of sensor MIL codes of course. I wonder if it's more engine than the transmission.
The speedo is working normally, not jumping around at all.
What should I be looking for regarding the the fuel trims. I did a scan of all the parameters yesterday and didn't see anything goofy. The weird thing is that when I first start up in the morning, everything is fine, but after things warm up a bit the problem comes back.
It seems like an electrical problem, which is why I thought it might be the speed sensor. But since the speedo is acting normally as is the shifting I think I can rule that out. And if there was any water present in the connector or sensor it has probably evaporated by now since once the engine gets up to running temperature that transmission housing gets plenty hot.
One thing I noticed that was weird was when I was in a parking lot I got the "blip, blip, blip" hesitation when I pressed the accelerator. I pulled over. popped the hood and manually activated the throttle linkage there was nothing. Sounded normal, no hesitation, which is why at first I thought it might be transmission related.
But now I'm thinking it is probably electrical, and there are a lot of sensors involved that could be faulty, or as you suggested something simple like a hose/wire that got knocked off.
I'll take a closer look today at everything and see if I overlooked any hose or electrical connector.
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