While I don't think its entirely correct (the board outline probably needs to be set as I have to increase the base board size in pcb to get the gerbers to work correctly), this part contains a working (but possibly misaligned because I don't have a board to look at 
) pcb. I had to scap yours and start from a standard part as yours has a bunch of unused elements (that I was too lazy to delete) and the copper groups are wrong and as usual Inkscape and I don't get along with making groups. The easy way to check alignment would be to put a piece of perf board on male .1 pins plugged in to the sockets. Assuming they line up correctly (which I would hope they do) then counting blank rows to the first pin of the various connectors will at least get the connectors correctly aligned. Also your script seems to have added a -2 to all the connector names (I removed them so pcb now works in Fritzing). Schematic is pretty close now, I can adjust it to be on .1 centers if you like.
Embedded Micro Mojo v4.fzpz (32.9 KB)
Peter