Much of the uncomfortableness of period shoes would be assuaged by woolen socks, and everyday use molding shoes to fit more comfortably. But sometimes, reproduction shoes just don't fit quite right. Many times, they aren't made to our feet and never fit perfect.
There are a few period solutions to the problem, the most common one seems to be an insole made of "kid leather" glued inside the shoe. This would make shoes a little tighter and could cover any uncomfortable stitches or overlaps. It is very simple to make this kind by tracing the bottom of your shoe onto leather and cutting it down as you need to make it fit.
For those who wanted a little more cushion, knitted insole patterns were widely published.
I've included 2 knitted patterns below. These patterns will have to be widened slightly to fit a modern day foot. If you have ever had the chance to look at period shoes, they are thinner than most of our shoes and feet today. The size of our feet is linked to our diets as children and modern people in general have larger feet even just compared to our grandparents. If you are a beginner, you can trace the bottom of your shoe to use as a template and increase and decrease stitches to match it.
I like the idea of sewing the knitting to muslin and sealing the outer edge with ribbon: