Wish you would have mentioned the batteries would have saved me some typing, lol!!! Also it is always advised to replace both at the same time, otherwise the weaker will draw off the stronger, but I am sure you know this being a tech, just thought it may help others who read this. Injectors usually don't work and then don't work or work only when cold so I would rule that out. Have you checked the oil level in the HPOP? Remove the allen head bolt on the top of the HPOP and see how low the oil level is. Should be within a 1/2" of the top. Your injectors are fired by high pressure oil, if your HPOP is leaking down to the LPOP it a can be a real pain to fire up, it may be a slow leak that takes overnight to leak down, would explain once it is fired up it does fine. Check this and let me know.
Are you sure your scanner doesn't need the PSD bundle software? Our trucks are not OBDII compliant and a OBDII scanner without the specific PSD software won't read the codes?
PS, if you think the Cummins don't have problems too you should take a look at the Dodge forum!!
NCH