I've never ran a Stage 1, but did run an open K&N cone style, basically identical to the Stage 1 AFE. I then went to a Scotty II... I don't wish that dam thing on my worst enemy. I now run an AFE S2 and it is sooooooooooooooooooo nice. There isn't noise unless I want there to be (ie, push the loud pedal hard), or unless I'm cruising at 80+MPH (common on freeway). Then it's just a slight whistle... nothing compared to the constant shriek that came from the Scotty.
Two things about the AFE S2... it's expensive, and it's ugly under the hood (big and pretty dumb looking). But after having the Scotty II it's such an improvement that it didn't matter.
And BTW, I had no change in EGT's going from cone K&N to Scotty II and same for Scotty II to AFE S2. I also run the Pro-Gaurd 7 filter in my S2. I also have a B-1-2 turbo that makes a lot of noise.