First, congrats on you choice to keep the rifle as issued and not bubba'ed.
and learning to use iron sights.
I'm not sure where, from your post, the bullet is impacting 100 yards. Most Mosin's shoot high.
Mine was 8 inches at 100 yards. I wanted it to be sighted at 100 yards when the sights were set at the 100 mark.
There are disputes what the 100 means, whether its yards, meters, paces, or what ever. That doesn't matter. I wanted my set for 100 yards without replacing the sights and keeping it "as issued".
You need to determine how much to move the sights to get it on.
Its not that difficult.
Measure the sight radius, (its been a while since I did mine but I think it was 22 inches.
There are 3600 inches in 100 yards (100 X 36) so we want to divide the sight radius by 3600.
22/3600 = .00611
Every movement of .00611 of the sights will move the impact 1 inch at 100 yards.
Again mine was 8 inches so I had to move the rear sight down (8 X .00611 = .0488 inches) .0488 inches.
If you are shooting high, you need to lower the rear sight .0448 (in my case) or raise the front sight .0488 inches.
You cant raise the front sight on the Mosin. So you have to lower the rear sight.
To do this, remove the sight from the base. (there is a drift pin that it pivots on that comes out easily. Turn the sight over and look at the flat side of the sliding part of the sight. If you mill, file or grind on that flat bottom it will allow the sight to be lower when it sets on the sight base, which will lower the rear sight.
I put my sight my milling machine and milled it down .0048. Put it back on the rifle and now it hits point of aim at 100. Plus when I set the sight at the 200 mark, its on at 200, same for 300 & 400. My range only goes to 400 but I have no reason to believe the sights wouldn't be on at farther distances.
Like I said I have a milling machine, most people don't. You can do the same thing with a file, being careful not to take too much off, and to keep the file flat.
When you put the sight back on the rifle you can't tell its been modified. The Civilian Marksmanship Unit has matches were these rifles can be used in competition. The CMP Rules require the rifles be ass issued but do allow the above modification to the sights because you are using the original rear sights.
Now the above was based on the idea the rifle shoots high. If it shoots low, you need to lower the front sight 0061 for every inch at 100 yards. That's not hard to do, you still keep the original sight.
If its off left or right then drift the front sight. If your shooting right, the FRONT sight needs to be moved right to bring the impact left, and if shooting right, the sight needs to be moved left to move the impact right (that's opposite of the direction one needs to move the rear sight, but the rear sight on the Mosin cant be moved left or right.
These rifles are old and crude, but they are shooters. Once one has the sights lined up, and learns to shoot the rifle, they are excellent shooters.