File the leading edge of the rear sight slide. This is how it was done when the rifles were originally zeroed. In any reasonable sized group of Mosins you will be able to find several that have been filed on the leading (forward facing) edge of the slide. Some have subsequently been blued, some are exposed steel.
During refurbishment, heavily filed examples are not "interchangeable" and would have been discarded in favor of new ones. This is a viable, but unpopular, alternative to the frequently quoted explanation that "Mosins shoot high because they were sighted with the bayonet attached". On occasion a refurbished rifle will have a slide with the trailing (rearward) edge filed which is the product of careless re-assembly or a "second chance". The slide is reversible so there are 2 opportunities for adjustment.
You have to remove quite a bit of material to lower the MPI 12 inches. I have one example where the filing was done while mounted; most seem to have been removed from the rifle to be filed (a pretty tedious process if you have to repeat it 3 or 4 time). Ideally you want to set the MPI just a small amount below the desired point so that the very fine adjustment can be made by removing material from the front sight post one file stroke at a time.
Much easier to add a piece of shrink tube
If posting pictures on this site wasn't so tedious I would show the evidence that the description above is correct. Take a careful look at you own example(s).