What I can say about the 5.9L ECM is the CPU inside it is more than capable of keeping up with high RPM's. For the technical people, the CPU is the same one GM use in their gasser ECM's from about 2006 up, these will run a gasser up to about 8,000RPM with way more complex computations than the Cummins ECM needs to do. The scaling in the ECM's RPM calculations allows up to 8192 RPM!
So the CPU speed is not the problem, it has been suggested the Injector driver circuits are the issue, that may very well be the case because the charge capacitors need 'x' time to recharge to be able to fire the injectors. Switching them too fast may indeed cause overheating of the internals of the ECM.
However, soon we will be able to log the pilot, main and post injection pulse times, if it shows even just the the pilot & main are being used up to 3500+ RPM then above this turning off the pilot (and post) increases the available time the injector firing capacitors have to recharge.
Even though the pulse time is much shorter on the pilot, if the injector only needs to fire one main shot it's going to give the ECM more time to recharge the capacitors.
Cheers,
Ross