Danelectro convertion

I'm converting my '91 U2 to a baritone. Just got the new neck today and I see the nut will need major work. The nut slots are roughed in,and when I cut them to my strings standard, the action will still be very high.
1.What should I use for files. I'm uneasy of using my nut files on this aluminum nut.
2.Should I cut the slots and then take the nut down from the bottom? That is......remove material from the bottom of the nut.
Thanks

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