So, I got the chicken door circuit board all soldered together and all wired up and had it on the kitchen table testing it. It worked great! Then I touched the circuit board and it never worked again. :(
Apparently I shorted something that ought not to be shorted and fried my Atmega chip. Since the chip at this stage was solidly soldered to the board, I decided to start over and do it "right".
I now have some 28-pin DIP (no, not a dip as in an idiot, but a DIP as in Dual Inline Pins) sockets and some more Atmega chips on the way. The sockets let me easily replace the chip just by pulling it out, should it get fried again. In the meantime, I'm laying out the board better. This is what I have:
On the left is the dead board after I depopulated it. On the right is the new layout with a new blue clock board. This new board, instead of having soldered wires, has header pins for everything. Also on order are some connectors to er, connect wires to the header pins, and a crimper tool to attach the connectors to wires. The connectors cost 3¢ each, but they make things far neater than the rats nest of 16 or so soldered wires that were coming off the old board in a snarl.
On the new board I'm also leaving 8 digital pins and 1 analog pin available for future expansion (Lemontree wants to add a feeder at some point).
I'm also applying electrical tape to exposed conductors to prevent any more face-palm mistakes.