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The advantages are that it gets rid of a little restriction in the exhaust outlet, it can no longer stick, and the actuator in the pedestal can no longer leak (I'm sure yours is by now). Can't really come up with a disadvantage, unless you like to start your truck and let it idle a lot when it's cold, and even then, mine does just fine.
A high-idle tune has nothing to do with the EBPV. The PCM will idle up the motor when the EBPV closes, but this is a completely separate thing. Your high-idle tune will work either way, and in fact, the truck will still idle up even with the EBPV gutted.
I can't see that thread, but you have a 2002. The early 99 pedestal won't fit. Just gut yours. It's a good, simple mod. I had a helluva time drilling the rivets off the shaft, but once I got those off, it was all down hill.
Oh yeah -- forgot about the exhaust brake thing. However, there are those of the opinion that the exhaust brake using the EBPV is hard on the engine. I don't have an opinion either way, but I can see how it's handy if you tow a lot (I don't). But it's probably a good tidbit of info, in case you're considering it.