Great thread!
Your Whitworth is an early one like one I got a while back. Mine, also .458 is just a couple months earlier, SN is 1000024 and those rifles started with the 1 so mine may actually be no 24.
Mine has the same features as yours, the 3 folding leaves whereas the later ones like my .375 had one fixed and 2 folders. You also have the early style barrel band and front sight as does mine, not many around of this vintage.
Sad to say mine came with a nice factory walnut stock that was damaged inside from recoil. I have made those repairs but it also needed feed and ejection work which I gave to a 'smith to do, its on its way home now. I dont share your skillset!
Whatever you do when you put it in wood, bed the hell out of it with good bedding, it really needs it. Mine was not bedded from the factory as it should have been and as my .375 Whitworth was, in two places. The main recoil lug area was bedded as well as a second lug screwed to the bottom of the barrel up in the barrel channel and bedded there, I recommend doing that. This is a good feature and after many rounds my .375 is still holding up well.
Were it me I would not be in a big hurry to plug those rear sight holes, you might want them someday and they dont hurt anything, put fillers in and forget they are there.
Following your thread with interest.