If you haven't got your answer yet...
You need to stack up all your stuff (you know, measure twice), then cut.
Put your whole bike together, put in your headset, install the fork, stack on all your handlebar stem spacers, stem, maybe more spacers, and the top cap - make sure you have enough spacers in there to make adjustments if you ever get a different stem, or rise bars, or whatever - 25-30mm spacers might be a little generous, but you can cut more later (you can't cut less later).
You should cut the steerer about 3mm shorter than all your stacked up stuff. Or sometimes the handlebar stem mfr. will recommend how much minimum clamp area is required within the stem (if there are no spacers above your stem, which is probably not recommended).
Hope that helps.
-F