So sand the spiral fluting on the bolt with the 600-1500 grit just to knock the edges down?
Also sand the rails and receiver? Or can I use the flitz polish on the receiver and rails and just work the bolt. I plan on removing the bolt head so I don't end up lapping the bolt face. Really I don't even plan on closing the bolt anyways I would just work it back and forth. It seems that spiral fluting gets caught up on the sharp edge of the rear of the receiver.
My personal preference is to use good quality paper backed by a hard backer, or hard stones for doing stuff to the action itself, but again that my preference
If your bolts catching on the sharp edge of the receiver, I would suggest breaking the 90° angle slightly. That won't stop it from catching a little, but it should turn a hesitation or stop, into a bump. If the edge that's catching is a flat surface, you can use a stone, or 400grit paper backed with a hard flat object to make a few passes at a 45° angle (45 is probably steeper than needed) to just remove the sharp edge. If it's the upper round portion of the bridge a round dowel of the correct size can back the paper. Again a few passes them check.
The reason I'm not a huge fan of using the abbrasive on the bolt approach is that you work the WHOLE contact surface, rather than the exact spots that need attention. Also since you'll most likely hold the handle the pressure is uneven, and with as sloppy as savage bolts are you can cause an un intentional ware spot.
Flitz is a very fine polish so would probably be least likely to cause this issue, but its also best for final finish rather than initial work.
As Troy said check to see where work is needed. If you don't need to do the rails or the inside of the rear bridge is leave it alone. My savage had alot of tool marks on the rails which would make the bolt chatter on the way home so I did polish them, but it's not always necessary.
Again remove your trigger when doing work on the action, also make sure you clean all the recesses extremely well after doing any abrasive work. You don't want left overs in or on the contact surfaces, especially the bolt lugs/recesses, or in the chamber.