A few changes had to be made to my board since I last posted, I had forgotten an important capacitor on the reset line. TTL serial programming on AVR chips requires a capacitor between the DTR line and the reset pin on the microcontroller in order to properly form a reset pulse during programming.
I also discovered that I lined up my SPI header backwards; all the pins are in the right order, but the PCB currently has to be turned backwards to fit it in-line with the LED strip. All these changes have been made and commited to the git repository.
Also just as an afterthought I connected the unused CTS line to an I/O pin. In the future someone may want to interface this board with another project, and this way the FTDI header can be used as 3 I/O lines, two of which are connected to the UART system.
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Programming of the bootloader was done with a USBtinyISP by inserting the programming pins into the SPI header and the reset line on the FTDI header. The MISO line was connected to the exposed pogo-pin pad on the board and held there during programming by hand. The fuses I selected can be read from the table on the right. Once the bootloader hand been flashed the FTDI header could be used to program the board in the standard arduino environment (the board was flashed and programmed as a Diecimila/Duemilanove w/ 168).
The program I uploaded as a test was a simple rainbow pattern taken from adafruit's demo code. Due to my omission of the DTR capacitor I had to add one between the FTDI header and the actual FTDI cable I was using. New versions of the board will have this included.
Below is a video of the system working with the test program. Partway through I bump the ground line by accident and it briefly disconnects. The LED strip dims but does not go out during this period. My explanation for this is that current is being returned through the data and clock lines and smoothed by the capacitors built into the strip. Its nice to know that the microcontroller can actually sink enough current to keep the strip running without destroying itself, but I certainly wouldn't suggest trying to operate it this way.