Here is what I have learned over the last few years of toying with the 6.4L.
1. Cruise can be disabled by any fueling related DTC. If you are running a big tune, you are likely on the verge of draining the rail. This will cause a P0087 code. Now, that code takes 2 consecutive key cycles to illuminate the CEL on the dash. So you may not see a code, but if you go to pass someone and lay into it a little bit, internally the ECM is throwing a fault for rail pressure being out of range low. Because this is a fuel related code, ECM cuts cruise until the next key cycle, at which time the diagnostics for P0087 runs again and passes. We have toyed with modifying the rail pressure hysteresis levels so that the code doesn't get thrown internally, but it seems there are a few more pieces to the puzzle. We need to spend more time on it in the future to learn all the ins and outs.
2. Cruise has literally hundreds of thresholds and control parameters that make it function. As an outsider it may look really simple to make a vehicle hold XX speed, but to make a computer smart enough to logically do this, and safely, is a BIG amount of code.
When an aftermarket tuning company tunes a calibration for a truck, they rarely tune EVERY calibration ford releases. To date there are about 200 different flashes on the market for the 6.4L Powerstroke ECM. To maintain tuning on these calibrations would take a team of engineers working solely on tuning and maintenance (nearly impossible). A waste of time if you ask me. Instead, a generic base file usually used to tune trucks, and modified to work with multiple vehicle configurations (gear ratios, fuel tanks, tire sizes, GVWR, up-fitter packates, etc.)
Many of the cruise control conditions that must be met are speed/gear position related. By using a base file for trucks, some of the base values may be incorrect for your vehicle, kicking one or multiple cruise control parameters out of range, and killing your cruise. The ECM calculates a gear position based off of speed/rpm values and a known set a gear ratios programmed in the calibration file, and thus can calculate when it is in or out of range. (yes it uses the clutch switch as part of the input to these calculations, so shifting "dry" can help cruise remain operational)
We, at H&S, have been trying to get our hands on an manual trans 6.4 for some time now, but have yet to come across one local. We almost bought one a few months back, just to universalize the cruise control functions to work across all variables, but then got busy with some other projects. If any of you are close to Utah, we would gladly pay your fuel costs to travel out here for a day. It should only take a day or so to throw a couple of test files to the truck to diagnose what parameters are being thrown out of range, and provide a fix for it. Let me know if any of you are interested, and we will schedule something! I know it must be frustrating when the cruise does not work, and we would love to provide a fix!
Hope that clears things up a bit!