.25-35 or .30-30?

[Jack]

If the rifle is a takedown, you can interchange barrels if you can find them (after you remove the forend, open the action and the barrel unscrews by hand).
You might check with Gunpartscorp for barrels, either old or new. I suspect, though, that you'll have to have a barrel made, or the original barrel rebored- I'd check the price of both.
You might end up with a real nice multi caliber rifle set up.
The 7-30 Waters would be a fine deer caliber, although the original takedown model was never chambered in that caliber.
Both the 30-30 and 25-35 should work ,too, with the 30-30 having a bit more power.
The caliber the 99 takedown's were chambered in that I suggest you avoid is the 303 Savage. Brass and factory ammo is no longer available, and the 30-30 will do anything the 303 Savage will do, so the 303 just isn't worth the bother.
If you'd like to go in another direction, the 38-55 would also be a possible caliber. Not nearly as flat shooting as a 7-30 Waters, but it makes a nice big hole.