There is a very experienced gunsmith who frequents LRH (username: shortgrass) who will tell you not to have the bolt face or locking lugs squared because of the risk of compromising the case hardening. I have done those things successfully myself with a very light touch. OTOH, I had a different gunsmith do those things on two of my rifles and I am now replacing the bolt bodies.
A 98 mauser build is pretty straightforward. Put on a good barrel, a good trigger, and bed the action in a good stock and you will end up with an accurate, reliable rifle. Your parts choices and ideas of what you want will produce a very nice hunting rifle. Where your barrel is concerned, make sure to order it unchambered and unthreaded to allow your gunsmith maximum control over how the barrel is fitted to the action.
I have several rifles built on Mauser actions and they are my sentimental favorites. 30-06 is an excellent choice. Another one that may interest you is 338-06. I am having a 338-06AI built on a mauser action. I can't wait to take her for a test drive!