This should be straight forward for the test setup.

Place AVR on breadboard.
Connect your programmer correctly.
Connect some LED's and ofcourse power.
Write some code (see code on the left)
Look up the fuses at e.g. http://www.engbedded.com/fusecalc/
Get your fuses right.
make install-fuses
make install

It is a bit more specific with the board setup, as follows:

Place avr on the perf board and solder the islands and the reverse side.
Place pin/headers on the perf board and solders the islands reverse side.
Take the power board, add some pin/headers solder them to it, and solder the islands to the reverse side of the perf board.
Now I have an avr with headers next to it. on the perf board side connect the pin/headers to the avr pins with solder.
Now we have our basic setup on the board.

From there you can solder wires with female headers to the diodes and places them on any pin you like, as in you are free to change it later.
That, and, you can still program your avr if you need to, since you can just still connect to miso, mosi and sck if needed.

I didn't feel like doing the same to the ground wires of the diodes, they just go to 'a ground' on the board (see project picture).

I added a 9v battery lead to the power board so everything is powered, and adjusted the power board to 4.85v as that seemed enough to power the diodes/pattern well enough and not burn the avr or diodes to cinders. Ground goes to the 4.85v output ground side of the power board.

I used some nuts and bolt to squeeze the 9v battery under the components board by another board.

After adjusting power, I connected the output to the avr, and the system began to run.

Not that I feel very negligent about not putting in some caps for power, or resistors and transistors for switching on/off the diodes, or not connecting !reset, etcetera, but alas, avr's work their way through a lot of not-supposed-to situations. Good for us.

The final product needs a casing:

Found a transparant plastic sphere in two halves, that fit together nicely, and just glued the diodes from the inside to shine outwards. Taped the diode to the fibers, drilled a hole big enough so I could lead the fibers through said hole. Connected the battery and watched the show :) have fun all, later!