Got it fixed, thanks a lot! I basically followed the thread with a box cutter from the good portion out. There were a few aluminum hairs that came out. Using the bottom bracket locking worked beautifully, thanks a lot for that tip.

Onto my other question; what would be a good rear axle to buy? The current axle is already slightly bent and I plan on putting a significant amount of mileage on this bike.

Funny thing about thread files, I keep seeing them on used stores here in Japan but never knew what they were for :**