Any of the calibers would be suitable for deer or coyote. The 54 is better for hog as they can get large and are tough and the extra whomp of a 54 will make the difference between success and wounding the animal. The extra felt recoil associated with the narrow buttplate of the late Lancaster may make shooting that rifle uncomfortable. An early Lancaster would be a better choice for a 54.
If you are comfortable with your ability to place your shot at a reasonable hunting range of about 50 to 60 yards, then a 50 can be used to take smaller hogs.
Since this is to be your first flint lock, consider the 50.
To be satisfied with flint lock performance, it's all about the lock. Get a Chambers lock or the Chambers' Deluxe Siler lock. The next step is to get a quality barrel, such as a Rice, preferably swamped. Because I'm letting a swamped barrel can be tricky, pay for your supplier to inlet the barrel. Is you go for a straight barrel, think about a 38" long barrel to take away some of the muzzle weight.
Now depending on the tools you have, such as a drillpress, taps and dies for threading bolts, files and carving tools to finish inletting the lock, trigger, trigger guard, and ramrod pipes, it may pay to have the breech plug, underlugs and sights installed.
Extra premium wood is nice, but top performance from the components is what makes the rifle special.