As far as reboring goes, if the muzzle accepts a loaded 30-06 neck (.336�-.339� diameter) clear to the shoulder it is unlikely that it will clean up at 35 caliber. By the time you remove enough material to clean up the pits, it will be over the .350� finish diameter of the 35 caliber. Anything smaller is out of the question. The 38-55 almost always cleans up rotten 30-30 barrels and it was a standard chambering in the 99 at one time. You might be able to find a correct (38-55) cartridge rotor for your rifle and ammo/components are readily available. This is a cartridge of modest pressure which is well suited to a vintage rifle such as yours. In my experience, your old barrel having inconsistent diameters will not cause a problem as long as the new, larger caliber cleans up the entire length of the barrel. Your barrel will need to measure at least .579� outside diameter at the muzzle to have adequate wall thickness when rebored to 38-55. Any sight dovetails would also need to be evaluated for remaining wall thickness under them. If reboring is not possible then relining or replacement are the options to consider.
