[dipper]

I have never re- barreled a Savage model 99 -- I could be wrong, but I doubt the original barrel and action for that matter has square threads.
I have cut square threads but never in a firearms application.
You may just be seeing a poor thread job--standard 60 degree that is---with larger than normal flats on the top and bottom of the threads.
I would check to make sure what kind of threads Savage used on that rifle before I went any farther---maybe someone with experience with a 99 will come along and let us know exactly what type of threads Savage used back then--like I said, I could be wrong but I doubt square threads.
A Savage 99 is on my "must have one day" list--they are fine lever action and there is a rumor I have heard about Savage re-introducing it again--who knows?
Are you sure the original barrel is bent?? It takes A LOT to bend a barrel like using it for a crow bar and you would have to be pretty darn strong at that.
Just thought of something, did Savage offer that model in a take down--I think they may have and that could explain the threads.
You should talk to a smith that is familiar with the 99---I can tell you for sure that the rifle is sought after and has some value to it---I would think long and hard about altering it in any way.
If it is a take down model, a good smith can set you up with another barrel and you can deep the original.

Dipper