You can disable EGR in the tune very easily. Cheapest way to do this is from moates.net - you'd need the Jaybird J3 programmer $75, and an F3 module (the 'chip' that plugs into the ECU) also $75. You can use TunerPro (free, donate if you like) to do the programming. You'd need to locate a binary for your ECU online, since this setup won't pull your tune from your ECU. Once you burn the chip you just plug it into your ECU.
Alternative is Moates Quarterhorse, still $249 it seems. That one takes the place of the hardware above and pulls the stock tune from your ECU as well. You can use TunerPro with the Quarterhorse as well, or you can pay about $100 for Binary Editor which is probably the best software to do the tuning. With the Quarterhorse and Binary Editor, you can hook up your laptop to the chip and datalog and get real running data just like a more modern car, but also write changes to the tune as if you had an HP Tuner (and license) on the modern car. Only downside about the Quarterhorse is that it has battery-powered memory. That'll last you 5-10 years but I eventually burned my final tune to the F3 chip (which is more like flash memory, and nearly identical to an SCT chip) and pulled out the Quarterhorse for use in other cars.
There are 'remote tuners' you can find on this site that can do the tuning (and probably a whole lot more than just disabling EGR - like getting that 'matched' MAF and injector slopes properly calibrated, maybe even giving you a bit more power) for you if that all sounds too complex. Tweecer's still out there and can do all the same, it's just a lot more expensive compared to Quarterhorse (especially if you want the version that datalogs and reads tunes like Quarterhorse does).
It's literally one value in the tune, Scalar EGR System Type to 2 to disable it. Please note that the above all assumes you have a Mustang ECU - if you don't (came from the Explorer) you'd need to make sure whatever you buy supports that ECU.