LTK:
Are you able to post good clear pics of the front and rear sights? You will need to upload them to a photo hosting site then post the link here.
I ask because there may be enough experience amongst the forum members here to suggest which of the sights (if any) may be a replacement, and how best to go about modification.
Many of us own vintage Alex Henry double rifles with which to compare your example.

I will add that shooting high with modern regulating loads is not uncommon amongst express rifles, but usually it is the bullet striking in line with the top of the bead, rather than under the center of the bead, perhaps 4 to 5 inches high at 50 yds, but yours sounds like its much higher.

Personally I prefer fitting a taller replacement caterpillar front sight rather than filing anything, but wouldn't hesitate to file-in a rear sight if it could be done in a way that retained the original lines.
Nothing worse than the top half of the "100 yds" engraving filed away...