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The easy way is to simply unplug the EGR valve. Some people install blocker plates where the exaust from the EGR cooler enters the ypipe, some a modified ypipe that deletes the EGR exaust pipe entering the EGR cooler (my method), and some remove the entire EGR cooler. As for the EGR valve, leave it be or if you wish, weld the plate in. Either way, it works the same.
On the '03 and '04 models there is a throttle plate after the elbow. To my knowledge there is no need to remove the plate, most people do not. However, having anything in the way would be considered somewhat restrictive, so if your plans are to go racing, then remove the plate. If the truck is your daily driver, there is no need to remove the plate. I have considered removing mine, but I don't want to deal with the dealer if I have to take it in, so to this point I have left mine in. It would be nice if Matt (PSD 60) would chime in as he has done tons of research on this.
If a dealer goes that far to try to void your warranty over something that was removed from the strategy soooooooo long ago then you have a pretty cheap dealer and you need to find another one. They would have to go to some lengths to even see it and even if you had major motor work it would be ignored. I removed mine because it was a restriction in the airflow. All you do is remove the four elbow retaining bolts and remove the 2 screws that hold the throttle plate. You should keep a magnet handy just in case you drop one of the screws down the throttlebody, but that's the only danger you face--IMHO. Shouldn't take more than 5 minutes to complete. If I had $150 I'd buy the accufab elbow for the later model and take the plate section out all together to get rid of that stupid shaft that goes across the hole, but that's being just a little ****--lol.
NPC, are you sure the elbow works for the '03 '04 models with the plate removed? I have wanted to try it, but I didn't want to blow 150 if it wouldn't work. I am kind of a freak about the best performance, whether it being for the mileage increase or for destroying the annoying little civic next to me .