I would not suggest any type of power sander unless you are REALLY good with them. File down the pearl close to the board and them radius block sand the rest. If you want to bring the shine back to the pearl, use 0-0-0-0 steel wool. Works like a charm.
I always leave a little shell over the top of the wood. I want to sand the shell down to the wood, not the wood down to the shell.
I agree with the .06" comment. For a fretboard always start with thicker material.
The piece pictured below had three different thicknesses of material on it. The brass was the thinnest .05, with the pearl and other shells at .06, and the stone being the thickest at .14. But, as you can see it all worked out right in the end.