First - you your are going to use it in your state for "primitive hunts" - check with your DNR to see if there is a "minimum caliber" for RB hunting. If you hunt deer in MI, I believe it is a minimum of 45 caliber IIRC.
As far as the other game you list - I've taken a lot of squirrels, rabbits, etc. with .32, .36 and even some husky woodchucks as well. If I personally were going to build another one for small game, I'd go with a .40 as it is a good "all around" caliber - but that's just my opinion. It's not too big for squirrels, rabbits, etc. and wold certainly take a coyote at a reasonable distance. After all, between the three calibers, you're talking .310, .350 and .390 round ball - not such a terribly large variation.
I'm 65 and my fingers just don't work as well as they used to for .32 due to the small ball size. I have a .36 under hammer and just the small difference in ball size makes a world of difference when it comes to me "fumbling" with my fingers to load. For squirrels, etc., it will do the job just fine but when I used to hunt tree rats. I didn't shoot unless I could get a good head shot - sometimes I was lucky, other times I missed!
I made several full stock rifles (42" barrel - Green Mountain barrels) in 36 using a 13/16" barrel - they were good rifles. My brother made a full stock with a 42" G barrel in .40 and it is a well balanced rifle and a great shooter for both game and target. I liked it so much that I have a .50 GM 42" barrel in my "stash" that eventually I'll make a full stock "poor boy" with and use a small Siler flintlock with it.
It kind of all boils down to what "you" like and what you'll use it for. A lot may also depend of if you already have a barrel or if you can find one in the caliber you want. Either the .36 or the .40 would be good and at the right distances, a .36 with good shot placement should take a a coyote down if you have enough "oomph" behind it.
Another thing to consider - a .36 will require a 5/16" ramrod while the .40 will allow you to use a 3/8" ramrod. In the field, the larger 3/8" ramrod with the .40 allows you to shove the round home without too much worry of a broken ramrod in the field. A 5/16" ramrod - not as "hefty" and more chance of "bowing" while loading and possible breakage - don't ask me how I know that!
Another option, if you can afford it, would be to make you rifle so you could have interchangeable barrels - a smaller caliber for small game and a larger caliber if you intend to hunt deer with it. Just remember that a larger caliber will mean a greater measurement across the barrel flats so you'd have to find a small caliber barrel the same size which wold of course add weight to the rifle with a small caliber barrel on it. And of course the diameter of the ramrod will have to be so it cold be used on both calibers.
Good luck to you and have fun! Nothing like the feeling of accomplishment in making you own rifle!
