I’d like to make these smaller to give some away. Any ideas of how to estimate how much dough to set aside for the bones?

I agree with AJ to make one batch and see for yourself.
In addition to or instead of the lime size ball of dough and weighing it, you might estimate by how much flour is in the recipe. A similar bread at allrecipes uses 3c flour and serves 12.
By extrapolation, this one which uses 4c flour may serve 16. So maybe make 16 small or 8 large bones as gifts.
https://www.allrecipes.com/recipe/7224/pan-de-muertos-mexican-bread-of-the-dead/

First weigh the dough once it's ready to shape, ideally using the grams setting. Then, pull off a piece the size of a large lime (what's recommended in the recipe for forming the bones). If it seems like the size you want, weigh it. Use that weight to figure out how many you can make by dividing the total weight by the weight of that first ball of dough. It probably won't be exact, so do the math to come up with the right number of bones, without an odd scrap left over. You may need to add or subtract to the ball you first weighed. Then weigh each portion for shaping. ;o)