I'm thinking that trajectories between the two would be so much alike that on that basis one would not out range the other, especially considering both would be used at ranges under 100 yards.
The bigger ball will have more energy at any range. Unless I was hunting grizzly bear I would not worry about the difference there. (in which case Robin's cannon or wall gun might be the best choice)
A longer barrel gives one a longer sight radius, which will improve accuracy, but a longer barrel, in it's self is not more accurate than a shorter barrel. All things being equal, a 10" barrel and a 50" barrel, both with a 50" sighting radius, would have equal accuracy.
Generally a longer barrel will increase velocity, which can increase range, especially with heavy charges, but the difference between a 46 and a 40" barrel would be very slight. You would see a more meaningful difference, in the long barrel's favor comparing a 30" barrel to one of 46". (or a 30" to a 36") Adding 6" of barrel length to a 40" barrel would see little gain.
I believe your 40" .62 calibre, when you have perfected your load, would/will plunk balls into a paper plate at 75 yards with the same consistancy as would a 46" .78 calibre musket or fowler. The .78 would hit a little harder when it got there though. As a .62 will kill Elk at 100 yards no problem, I certainly would not feel very under-gunned compared to the .78 with six more inches of barrel.
:no:
Rat