i suppose it depends on how or who does your modifications, and to what extent. on my brother's 6.0l we did an egr delete, and did it ourselves because we are too poor to pay for any labor. we basically took the stock egr cooler and drilled out the crap inside so that coolant would flow unrestricted through it. we welded a freeze plug into the exhaust end of the cooler. we took out the stock up pipe(passenger side), plasma cut the factory grove in it and welded a piece of sheet metal back on to it. the reason we did that is because the stock up pipe is half blocked off by another piece of pipe that is welded in right were it bolts to the egr cooler. that way exhaust is routed(forced) into the egr system. if/when you delete the egr, you will be left with(in my opinion) a major exhaust restriction. we also just left the egr valve where it sits. we wrapped the up pipes and down pipe in some funky low buck 2k degree lava tape and it works well. no noticeable mileage gains yet (we do hand calculate the mileage over a monthly 230 mile road trip we take, but thus far .3 miles extra i think may have been more of another modification we did in conjunction. besides we both have steeltoe boots.) but the jump in throttle response and less turbo lag is certainly noticeable.
oh yeah, and with some of the saved money, we had to invest in the bullet proof diesel oil cooler.