I assume this is a threadless setup,and these comments refer to threadless.
Since the steerer needs to be 3-4mm below ther top of the stem (or spacer) anyway,maybe you can find a stem with less stack height.Failing that.Stein makes a stem facer that is designed to square the stem.If you can remove 2-3 mm's total of both sides from the stem,it should be fine.I doubt that many bike shops have this tool,tho.
You are on the right track,considering both the headset and the stem.It sounds like you only need 2-3mm's.