If you really want to make an "accurately intoned" flute out of anything, the simple books commonly cited - and generally available, are:

The Amateur Wind Instrument Maker Revised Edition, Trevor Robinson, University of Massachusetts Press, (c) 1973, 1980, ISBN 0-87023-312-2. My copy was about $18 US a couple of years ago.

and:

Making and Playing Musical Instruments, Jack Botermans, Herman Dewitt, and Hans Goddefroy, University of Washington Press, Seattle, (c) 1989, ISBN 0-295-96948-2, Mine was about $19 US 6 or 7 years ago.

The information left out of these books is that you need to make one, tweak the holes as much as possible, recalculate, make another and throw the first one away, then repeat the whole thing about 3 times.

If you are making a Native American flute - tradition is that each player makes his own, and then invents his own melodies to fit his flute. They are rarely anything that approaches being tuned to a "standard" scale. Holes should be drilled to fit the fingers of the one who's going to play it.

You can "tune" after the holes are drilled, by enlarging a hole. If you elongate it in one direction or the other, you can make a fairly large change in individual note pitch; and simply increasing the diameter slightly in a concentric manner will also affect the pitch. Since this is about the only adjustment you can make - and you can only go one direction, it's well to start with fairly small holes and work you way toward the note(s) you want.

There are some good "standard references" that are easily accessible if you really want to make a "real" flute. The above two are not ones I'd bother with if that's the intent; but they should be quite suitable for what you indicated as your problem.

John