It works! (Mostly.)
Above are the images of v0.2 and as you can see there has been some basic reworking done to the board. First and most importantly I had to replace my original TO-92 78L05 with the TO-220 package because my circuitry required more than 100 mA which I had overlooked. Also I designed the board to be two sided, but because I can't do through plating at home I had planned on top-soldering. This turned out to be very difficult for some components. So I gave up on that and just soldered wire-wrapping wire in place of the top traces.
With this module, I finalized the code and thankfully included an ICSP header to program the board which made life a lot easier. After I got a basic design working I wrote a Processing sketch to upload new designs to my module via the serial connection.
Schematic for v 0.2
Board for v 0.2
The next step for this project will be to order the parts for the modules and then send out the board design to be manufactured. After all of that is done, I will finalize the design for the programmer and manufacture that.