Simple answer: If its deleted, the EGR system will be disabled as well. Easy way to check this, unplug the EGR valve and see if the truck comes up with EGR codes. I don't know of any delete tuning that leaves the EGR valve in operation, its kind of an all or nothing deal. I would skip the MM at this point, they are outdated and you more than likely got one of the knock-off clones as H&S has been out of business since like 2014.
First thing I would do is get some EGR block off plates, last thing you want is one of the coolers to start leaking. its also best to leave the lower cooler in place after installing the block offs to support the crossover pipe.
Tuning wise, these days its pretty much all ez lync and SCT tuners. Its just finding custom tunes that is hard, and its gonna be on you to figure that hurdle out.