Etching the board: This process was divided into to parts
Turns out I have too big of hands to solder, so this was painful. And aslo it took some time for me to master a few tricks.
In my first board my technique was wrong - scooped solder and placed on components "legs". This did not work at all, and did not even get a red led when connected to the programmer.
I went on to mill my second board. This time soldered super elegantly, except for one mistake that skrewed-up my board. Tried to extract solder using the copper thread... but intsead of pulling away quickly, hesitated, and when pulling out a good piece of the copper when right off with it.
Programming the board:
After a third section of soldering, I went on to program the board.
At first MAKEFUSE gave back an error. Check Makefile and changed the programmer from avrisp2 to ice-something.
Finnaly, desoldered the SJ1 and SJ2.