If yo live in an area where you can do it without emissions testing, I would delete the EGR system. The kits aren't that expensive, but then you have to add a programmer. Since yours is no longer under any kind of warranty, that shouldn't be an issue(of possibly voiding it). There are programmers out there that will just turn off the 'CHECK ENGINE LIGHT' when the delete is done. However, do not add any horsepower with a tuner unless you put head studs in the truck or you will blow the head gaskets. Then you are looking at a 'cab off repair' Around here, diesel shops are charging around $2600 for the head stud job. Much cheaper than a dealer. If you go ahead with a delete, coolant filter and putting in head studs(I recommend ARP), then you will have pretty much 'bulletproofed' the 6.0 and it will have a much longer and healthier life.
2012 Sandpiper 365SAQ weighing @ 15k, Onan, 2nd air, slide toppers, TST
2013 F350 6.7L Lariat 4x4 CC DRW,Viair 1007, Ride-Rites, Edge CTS, B&W
2001 Chevy 3500CC DRW 4x4, 8.1L, 4.10 gears w/ Detroit TrueTrac
2001 Ford Excursion Limited 4x4 7.3L,V/B Spring Mod, ProComps, Hellwig Swaybar, & other 'Necessities'