I just purchased a 2008 F350King Ranch with 230K on it. I bought it cheap after the dealer tried to return it to stock and found it didn't run worth a crap when they did. The truck came with the EGR deleted, I deleted the DPF and installed a H&S Mini Maxx with the mildest tune settings. Since I have had the tuner installed it has on 3 occasions (in like 2000 miles driven) had a CEL with the same pair of codes:
PO40D-Exhaust Gas Recalculation Temperature Sensor A Circuit High
P0128-Coolent Thermostat Performance
Every time this has happened it is on startup after a run down the highway, but no correlation beyond that (once over a mountain pass, once just down the highway 20 miles, never towing.) The truck has a Sinister EGR Delete that came with the truck, and the temperature probe is plugged in and tucked above the fuel filter, I assume needing to stay plugged in like the EGT sensors after the DPF Delete, and it has never seemed to get very hot where the sensor is laying. Any ideas?

I also do not get correct Pyro readings. With the Pyro set to "Factory" Pyro 1 always shows 92F and Pyro 2 shows usually 165F-185F. I read that it needs to be set to "H&S Pyro" but that setting makes both gauges read 0F. Is the 180ish reading for Pyro 2 about normal and I have a crap sensor for Pyro 1? Which sensor feeds this?

I appreciate ya'lls help, I've done a lot of searching and solved all the other issues the truck had, but these baffle me.

 

Looks like your not running a EGR delete tune possibility, second the egt 1 and 2 are generally the pyros used on the DPF system you should be looking at the EGRT sensor. Im not overly familiar with the H&S tuners but these might be some things to check.