kinda sounds like the tuner prob took out the FICM, or helped it down the path it was headed. if you know some one with a scanner, get them to scan it and check for the P0611 or any/all injector low voltage dtc's which means you need a FICM. or you just happen across a HP oil leak. either...
you could have an injector(s) failing after cold soak period, if an injector is failing you might be able to notice a slight misfire when under heavy load during accel. your best bet for having something figured out is take it to a dealer late in the day and leave it overnite for them.
EGR and Oil cooler blown and you could have a possible head gasket issue do to overboosting from the programmer, causing the heads to lift and take out the EGR and Oil cooler. Replace EGR and Oil cooler, then re-test for HG failure.
sounds like the STC fitting on the high pressure oil pump came apart, common issue on the 6.0L. Best route to take is tear it down to check the STC fitting condition and replace as needed.
try unplugging your ICP sensor and see if it clears up when its idling. also try wiggle testing the ICP and IPR pigtails when idling. You could possibly have the IPR going out.