Timing seems to be the biggest factor, but have seen sometimes where main pulse is changed at idle along with pilot pulse and cause a small lope to it from fueling heavy. I wouldn't disable it except after 2800rpm (WOT as thats the only place it needs to be disabled then base all your fueling off of main injection pulse and 1 timing table. (for ease of tuning and a little more fuel pressure from not having multiple injection events.
On your truck (I think its an lb7/lly) You would go into the pilot injection tab, then go to injection quantity. Turn the 2800+ rpms and 80mm3 section and on to 0. Iv seen a few trucks pick up some rail psi