I so agree... My SG sounds really fine with its upgrades. People come up after the show and ask me about it... which means it's doing what it's supposed to be doing, making things memorable. I love the cleans, and I love what happens when I step on my Blues Driver. Good choices in stealth mods.
When they do the pleking, they cut the nut, so why did you get a new nut and mess up the pleking? Maybe I'm wrong but I thought that was part of it.
My nut slots were already cut a little too low. I told them to Plek it anyways. I got the new nut after the Plek job BUT it does not affect the frets in any way. They Plek'd the Frets and got them perfectly level. Adding a new nut does not undo what they did to the frets. They remain perfectly level. Replacing a nut simply adjusts your action at that end of the fretboard. No different that adjusting the action by lowering/raising your bridge. The frets are not touched when a new nut is installed.