Tom,
Since you already have witness marks(if not, no problem to make anyway), you will not have headspace problem, as long as you line them up at final assy.Actually, it would take a good bit of misalignment between the witness marks to hurt,it would show up on the sights first(for 06, the difference between "go" and "no go"qauge is 6 thousanths).I use aluminum blocks in my barrel vise, and clean both the barrel and blocks with acetone(every time).If the blocks are pulled up tight, they won't slip.If they happen to slip because not tight,the few aluminum smears are easily removed with WD40 and 0000 steel wool.I have tried hardwood,lead,abrasive cloth,rosin, and other methods;for me nothing worked better.I also remove the barrel when rust blueing.
Mike