So I'm finally going to do it.
I found this article through Hack-A-Day that said (among other things) that you can use
Testors Transparent Candy Emerald Green Spray Enamel as a solder mask that also protects the PCB traces from corroding over time.
Nurdrage's Videos on PCB Etchants was very useful in selecting an etchant. At 3:33 he specifically talks about Copper Sulfate and Hydrochloric Acid. I have both of these in my chemistry lab, so that's the path I chose.
The next required piece is a copper plated board. Hello Radio shack.
2-sided copper clad PC Board
I found this page http://wild-bohemian.com/electronics/flasher.html that has a dead simple LED flasher.
2 caps, 2 npn transistors, 2 leds,4 resistors. It's perfect.
I'm an electronics noob. So first I built this in the Java Circuit simulator from http://www.falstad.com/circuit/.
Now I'm building the PCB layout in Fritzing, a Breadboarding/layout tool. Thats the topic for the next post in this series.