You can do both at the same time. You will need to use tape on the barrel and tang to set the height of the action. Setting the height before you do any of your stock work will insure that the finished product will look as factory as possible.
As far as keeping the action square you should be able to line it up with the stock visually and the tape will help you center the barrel in the stock. Come to think of it if you wrap tape in two places on the barrel (front and back) if should self align. You might also want to view some videos on the subject as well.
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