You can delete the EGR, you just have to block it off at both ends. I deleted it on my old Mustang because of the long tube header I installed, never saw any big difference in anything.
As for the water line, you can ONLY remove that if you block off the passage where the manifold meets the head. Otherwise, coolant doesn't circulate properly and it creates hot spots.
I deleted mine (EGR tube) as I did the ranger header swap on both the '93 and '88. It will help as it keeps the crap out of your intake manifold. just cut the tube - leave about 12 inches on both sides
hammer the tubes flat and fold over to make a good seal.