Not sure if you're following the discussion in the Savage forum, Mitch.

But it looks like the two holes have been narrowed down to a side mounted old Noske 2.5x scope from the late 30's, or possibly a Boone mounted scope (probably from the same time frame).

Here's an old picture of the Noske mounted on a Savage 99T from the late 30's.

Originally Posted by Loggah
They are for a Noske little imp scope similar to a boone scope, there is a picture of one mounted on a savage 99 in strobels book, i will try and get a picture posted later today. Looking at it the holes might be to close or not? heres the pic.

[Linked Image from pbase.com]

“The Savage 99 Pocket Reference”.
All models and variations of 1895’s, 1899’s and 99’s covered.
Also dates, checkering, engraving.. Find at www.savagelevers.com