My guess is that the bolt was modified to have a cocking-piece sight installed.

It is time to remove the barreled action from the stock.  It may be one of the Stevens-Pope barrels, which could be fitted to any action.  Look for a "Stevens-Pope" rolled stamp somewhere on the barrel and probably a serial number on the bottom, opposite the rear sight.

The barreled action could also be a sub-caliber adapter for a field artillery piece or for a naval gun.  Krags were modified for such purposes.  A .22 caliber adapter would be a pretty good training device for a National Guard artillery unit when bad weather kept the troops in the Armory.

My only idea about the odd holes in the stock is to ask if anyone has seen a Hollifield Dotter or similar device used for explaining sight settings to recruits.  The rifles were held at shoulder height in some sort of metal frame.