Uneven custard cooking
I'll start by asking basic questions to make sure we all know what we think is obvious.
if the oven is calibrated? If so then bake them at either temp until set. Whichever you find best because high temp, shorter time, low temp longer time . If the oven is not calibrated that would be a good thing to have taken care of.
From your post you say they are not baking evenly. Your oven may have hot spots and the custards may benefit from being turned around half way through cooking.
When you fill the pans with water, is the water hot? If it is cold to begin with, the time will necessarily be longer. Remember the custard dishes will absorb some of the heat from the water. If cold water, everything takes longer to heat.
And of course regardless of the size dish, the two eggs per cup of milk remains as a standard custard recipe.