If you have the EB wired back thru the factory wiring to activate the EB and you have updated the TC to a lower stall that will throw off the engagement. The ECU is completely responsible for putting a signal on that wire that the EB picks up, if the ECU decides it doesn't want to acivate it based on APPS, wheel speed, and engine load, no signal. In order to get it to activate correctly you may have to have a 0 APPS reading for certain time period to get it to come on. One of the totally annoying things about using the facotry system is it has NO idea what you have done to the transmission to make it better, it STILL thinks it has the saem sloppy stocker in there and behaves accordingly.
Your trans really did you no facvors with a triple disk and no billet input shaft. Bad mistake on these later model trucks becasue of the shift\lock algorithms they have. That may come back to haunt you.
The ECU has no way of telling a shift kit has been put in. It does not monitor or read any of the pressures chnaged by a shift kit. It also has no way of knowing you have a more efficient TC or if the TC clutch is locked. All the ECU can do is set gov pressure and read it. A good shift kit will not materially affect the gov pressure. If it does, not telling the differences that can show up. The ECU cannot tell of the TC clutch is locked, all it can do is tell the solenoid to activate.
The facotry tools, and some others, can read the PIDS for demanded gov pressure, actual gov pressure, and lockup demand. None of them can tell if those functions happened correctly, only what it gets for feedback based on other parameters like wheel speed, APPS, and a calculated engine load. You can track these to see if there is an issue with them but it would take a tech VERY familiar with the software to say that this particular reading is going to effect the ECU demanding EB activation, that is almost an engineering question.
Short answer is once you build the trans like that you might just as well expect to use eithe rmanual control or a spearate controller for the EB as the factory controls WILL have some discrpencies.