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Well shortening the neck would also have the effect of shortening the scale length (with most nowadays being at 25.4" and a few (usually 12 fretters) at 24.9" - but the different scale length will affect your ability to drop/change tunings.
I do believe that adjustments to the nut and saddle are probably the way intonation is adjusted on the guitar. Definitely not a do-it-yourself thing unless you're a luthier/repairman or aspiring luthier/repairman.
Why not head down to your local Acoustic Guitar shop (we have a couple of wonderful ones in my side of L.A.) and see what they charge?
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