Figures that I can't find the right tools when I need to but this should give you an idea of what worked for me. I bought a MIK Squier Jazz Neck off of Craigslist that had a stripped nut and was able to remove the nut using short screw extractors like these. I bought mine from Harbour Freight but you can probably get them from Sears or any other place that sells tools.
They have an aggressive taper and reverse helix that will bite into the sides of the nut when turned counter-clockwise.
They need to be the short screw extractors. NOT the long ones. Unfortunately I couldn't find the set that I bought and just had some long ones laying around for these pictures. So in the next few pictures substitute the long tapered extractor for the short ones pictured above. The short tapered ones will bite into the sides of the stripped nut before bottoming out where the Allen wrench goes. The long ones will not and will bottom out before getting a bite. If I can find the short set I have I’ll edit the pictures and post.
Make sure you remove string tree and the tuners needed to get a straight shot at the nut. The key is to have the screw extractor bite into the stripped nut nice and square.
Here is a picture of everything. The 1/4 drive ratchet, extension, screw extractor, and the removed nut at the end. Of course your setup won't have the nut at the end as that's still in your neck.
Here is a shot with the ratchet, extension, and screw extractor in place. Once again make sure you remove everything needed to get a straight shot at the nut.
Here is the extracted screw from my neck
When the screw extractor bites into the thin walls it may bulge them out slightly and it might score the sides of the walls of the truss rod opening. I haven't cleaned mine up but with a little sandpaper and some clear lacquer or brush on poly you should be able to make it look good again.
I hope that helps. If you got any questions let me know.