'Stoney':

My theory is that your Krag, during its life, has been fitted for two different Receiver-Sights.

Its first commercial sight was a Lyman #33 or #34 for the Krag. The two sights have the same hole arrangement. (The difference is that the #34 has a 'click' adjustable windage knob).

I have marked your photo to show the diagonal holes that would have been used to mount the (#33 or #34) sight. The 'arrow' shows where the Lyman sight's elevation lever rubbed on your stock.

I have not quite figured out the lower rear hole.
(It is a very odd alignment, if the lower rear hole was used in conjunction with the front hole).

Maybe, just one screw was used to mount a different and later sight at the lower rear hole? (The Lyman model 48 - K, might be a candidate)?

The Krag version of the Lyman #33 & #34 sights show up from time to time on ebay. They are rather expensive.
IIRC - There may be two different elevation slide lengths available.

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