Hey just a suggestion for you.
On your pads for through hole components change the pads to have holes in the center. It makes it much easier to drill when there is a center hole to line up the bit, kind of a pilot hole. Other than that they look great. It is hard to beat the presensitized transparency method for good quality low run home made boards prototype boards.
Prices are pretty reasonable for professional boards now days so when you have things working pro boards are a no brainer..
When the going gets weird, the weird turn pro.