You say it hits 1000°F in 3 seconds when accelerating to 55-60. I'm assuming once you let off the accelerator it drops back down quickly? Unless you're towing, you probably won't ever sustain that temp. I'd find an entrance ramp to a clear highway and gun the truck from a stop up to 75 or 80 keeping an eye on the pyro (better yet get someone to ride with you and watch the pyro so you can pay more attention to the road). If you don't get over 1250, I'd think it'd be fine.
If you do tow, I'd hook up whatever you pull, take it up a couple hills nearby driving in your usual fashion and make sure you don't get over 1250 at all and that you don't go over 1050 for more than a few seconds.
If you find that the egt's are too high for your liking and you want to do something:
An abundance of fuel relative to the amount of air you're flowing (think black smoke) will yield higher egts. To lower your egts you have to either increase air flow or decrease fuel - which will also cost you power.
So turning down your pump will lower your egts, but you'll also lose some power.
I'd see if there's anything you can do to the air intake and filtering or exhaust to get better air flow before turning down the pump. 3" exhaust may be bigger than stock, but it's still probably not optimal for a turbo 6.2. My duramax (6.6L turbo) had 4" exhaust to the muffler where it switched to 5" (not stock though - 400+ hp). A new clean filter or a better flowing one from amsoil may surprise you.
I'd also leave the thermal wrap you've got. It causes your egts to be higher, but it helps your turbo efficiency. Pre-turbo is not really where you want to be losing heat for the sake of lower egts. You'd rather open up the intake and or exhaust if you can. Then look at turning the pump down.
Spend some time here:
http://www.thedieselpage.com/