Any thoughts why the butt stock has the extra holes in the end from a different hole spacing.
The BP seems to have been on that stock since forever
Just a guess, but maybe your gun had the original buttplate replaced at some point due to breakage with the later style hard rubber plate with the simple incised lines. Had that been done decades ago, the present buttplate could easily look like it had always been there... until you see the second set of holes.
If you look at the two buttplate photos on Lloyds guns, the older gutta percha buttplate has hole spacings that seem located closer to the plugged hole and the unused lower hole in your stock.
Lloyds observation that your gun is a transitional gun roughly between Syracuse and Fulton production supports this theory. If Lloyd could measure the screw hole locations of his gutta percha buttplate, it might help support this thought. However, these old buttplates were apparently produced in different sizes to accommodate stocks with larger or smaller dimensions. I have several later type L.C. Smith buttplates in my odd collection of spares, but no examples of the older and more attractive gutta percha plate.
At first, I thought that a recoil pad with different hole spacing might have been installed without cutting the stock, and then the owner later decided to remove it and reinstall the hard rubber buttplate. But had that been done, the top hole likely would have been plugged with a dowel, and removing that dowel later would have left an oversize hole. After over a century, we are often left with nothing but educated or uneducated guessing.