With the EGR you won't get the full power possible with your plate. Will fall about 25 HP short. You should open up the exhaust and intake for better flow to keep EGT safe. You might want to take the intake apart and clean the soot out of the manifold, on mine the vac port to the turbo was plugged. I removed my EGR but if you block the vac line to the valve It won't be a problem. I also used a 2" speed bit on an extension and 'unplugged' the cat. It's still there but hollow.
I did mine upgrades in steps.
1. Disabled the EGR and started getting heavy black smoke under light throttle, not much boost at all.
2. Replaced exhaust manifold with ATS 3 piece and installed Banks Brake and their exhaust included with the power pack. Also, added AFE filter to intake. This eliminated the smoke from exhaust and EGT was 200-300* less than with factory stuff. Also, noticably quieter operation in the cab.
3. Installed plate and twin ram. This is when I found a pile of soot in manifold. When done what a difference in performance, no more flat spot getting on freeway and can run the Grapevine towing 6k in OD and at 26 lbs boost the EGT stays below 1150*.
4. Installed heavy exhaust valve springs for EB. . Replaced all 12 springs so I can go to GSK
Been running for 2 yrs and auto hasn't complained. I am getting DTT this winter so I can add injectors and other toys in garage. Towing is the only time I have noticed any real increase in MPG, about 3. Still getting 13-14 in town and 17-19 on hiway depending on right foot.