If you're going to remove your EGR then do it the right way. And remove the flow of exhaust through your intake completely. We have internal EGR systems, which means the exhaust comes in through the intake, up to the EGR spacer, through the valve (when open) into the intake tract. If you just unplug the EGR valve, or unbolt it and block off the holes, you're doing nothing about the superheating of your intake plenum! The exhaust gases enter the lower intake from only one of the heads, I think it's the passenger side. The entry is right in between the intake ports of cylinders 2 and 3. If you block off this passage to the lower intake, then you can actually see power gains (no more than a few horse really) due to the overall cooler intake plenums.
What I don't understand about this EGR removal and engine running problems. The Computer is using an EGR valve position sensor. If you disconect vaccum to your EGR, that sensor is never going to tell the computer the EGR is opening. Is this fact just ignored by the computer, and less fuel is injected anyway? Not that I don't believe such an idiotic system is below Ford, but this simply makes no sense.