Mr. Kelly, that is a neat gun. I'd just never remember all the gadgets, and wind up using it for a club!
I've shot patched roundball from a number of doubles over the years, and regulated half-a-dozen or so of them by filing the muzzles; I've got a regular routine established. If anyone wants to try this, be warned--it will usually really mess up shot patterns.
To keep it simple, I usually start with a ball .010-.015 under actual bore size, with .015-.018" patching lubed with neatsfoot oil. Shooting at 50 yards, start at 60 grains or so of FFg. Use the same hold on the target to fire both right and left barrels. Then load up and do it again. I suppose ideally you'd want 10 shot groups (five from each barrel) but I often do 6 shot groups until I think I'm close to the right load.
Work up in 10 grain increments. As the powder charge increases, the initial largish group opens up into two groups, one from each barrel. Measure the group size from each barrel and average them together; the load to use for regulation is the one with the best average group size.
After 60-80 rounds from the bench, that's usually all the "fun" I want to have for the day, so I return another day to double-check my best load and file the muzzles.
For instance, from a bench or post, my current 11 gauge gives me 2) 3" average groups at fifty yards. Granted, those 3" groups are about 9" apart, and one is a little higher than the other. If I wanted to regulate it for this load, I'd begin by filing the muzzles to first correct the horizontal dispersion.
Think of a target's view of the muzzle of the right barrel. From this perspective I'd want to file so the maximum amount of metal was removed at 3 o'clock, tapering away to none being removed at 9 o'clock. I usually take 1 or 2 file strokes on the right barrel, deburr the muzzle with a piece of wet-or-dry, then shoot it to check how POI has moved. Then I do the same thing on the left barrel (with the file removing metal at 9 o'clock but none at 3 o'clock). Shoot it again first to see how the barrel groups alone, then to see how the two groups have moved towards each other.
As the horizontal dispersion is corrected, some of the vertical dispersion will also be corrected (but some may be introduced). When the horizontal dispersion is close, you have to decide what if anything to do about any remaining vertical dispersion. If I have to do this, I tend to raise the POI of the low-shooting barrel, and leave the high shooting barrel alone. This is done the same way, by filing at 6 o'clock on the muzzle of the low-shooting barrel. By this point I'm usually shooting every half-file-stroke.
When the two groups are close to super-posed, I start shooting at different ranges. Usually, I wind up with a 3-4" group at 25 yards that is close to the sight on the gun. At that point I'm usually done for the day, and finish up on another range visit.
On the third visit, I check the groups from the previous day. By this point in the process, I'm making corrections with emery cloth wrapped around a file. At some point you just have to call it "good," or you'll be out there forever.
I helped a cousin set one a gun like this. He had one of the early Navy Arms 12 gauges; we adjusted the left barrel to group ball with the right barrel, while leaving the right muzzle alone for shot use. It's pretty much his "everything gun," and he is inordinately fond of it.