Tim:
What position are you in when sighting? It is all too easy to "crawl the stock" when shooting from a bench, that is extend your head way too far forward on the stock. That in turn puts your head and eye too high.
Check to see if you can get sight alignment while in a good straight up standing position. Mount the rifle with you head fully upright, then lean your head over a bit without craning your head forward.
When fitting new sights it's best to modify the least expensive part, i.e., the sight. Tools are a light hammer, brass drift, fine flat file, fine safe edge triangular file, caliper, prick punch and vise. Measure the barrel dovetail depth and length and write the figures down. I like to thin the base first, then work on dovetail length. Hold the flat file on your bench and slide the base on it, turning 90 degrees every couple of strokes to keep the cutting action even. Measure frequently, and stop when it measures 2-3 thousandths greater than the measured depth of the slot in the barrel.
The triangular file needs a "safe edge"- one side without teeth. Dipping the file frequently in cold water, evenly grind away the teeth. Now use fine emery held flat on smooth part of bench top to polish even smoother. Use this file with the safe side against the underside of the sight body to shorten the dovetail. Work from both sides, and only on one end. Use caliper frequently to check process. When you get close, it's time to final fit for both depth and length, just a couple strokes at a time, trying to tap the sight into place.
If you go too far and the sight is loose in the dovetail, prick punch a series of marks across the center of the barrel dovetail.
Good luck. A lot of the fun of muzzleloading is tinkering. Or, as Miz Fox once said- she was not happy with me over something- "Go fondle your bullets!"
White Fox