Probably not this, but think about checking it to rule it out: read the alcohol content of the fuel. If you have a flex fuel engine and are not running E85, and the alcohol content reads more than 10%, reset it. That will also reset the LTFTs (which I see you've already done).
There's a link in this thread that you can open to see who's around your area. Might be good for us to know where you are, generally.
Interesting, but I don't think we have any Marathon stations around Denver, so I'm wondering what refinery would supply either the gas or E85 product.
The only gas refinery in Colorado (Suncor - https://www.suncor.com/en-ca/what-we-do/refining/commerce-city-refinery) is just now starting to...
We have a couple of E85 providers around Denver, one being Alta Convenience that handles Conoco products. But the E85 there is clearly marked as "not a Conoco product." The there's the K-U-M & Go (LOL) that doesn't differentiate; not sure who provides their fuels.
Get hubs that have new speed sensors included.
I wouldn't entertain replacing the PCM until I ruled out all speed sensors. Recommend using a scanner that can graph all the speed sensors for comparison and smoothness of the sensor outputs. Like using a sweep hand tachometer, or an analog ohm...
As you are changing the fuel filter (old one out, new one not yet installed) you could rig up the output of the fuel pump directly to the pressure gauge. Run the pump and monitor the leakdown right there.