If you're sure you'll never sell it (and it sounds like you're pretty certain that you won't), I agree with BrocLuno and 451 Detonics: As others have advised, make darned sure your gunsmith is competent for the task at hand (drilling/tapping) and get the rifle the way you want it. Personally, I agree with 451 Detonics' preference for a good receiver sight (like the Williams "FoolProof") but if you really want it scoped, my advice is to choose one that conforms in terms of proportion to the configuration and planned use of the rifle. In the case of the Model 99, a compact scope will detract less from the little Savage's fine handling qualities and will look better after it's mounted. I think a 1.5X5 with a 1" objective lens would be well nigh perfect. And get it mounted as low as possible because all older Model 99s (and most other rifles of the era) were stocked with low combs/drops for use with the factory installed iron sights. High mounts (especially the abominable "See-Thru" type) will compromise a good cheek weld and cause you to stretch your neck in order to obtain a decent sight picture.
Good luck on your venture. You should end up with an ideal setup for hunting whitetails.