The fzp should be reasonably easy to fix. All the pins need to look like connector0: (the added blank is to stop the forum from thinking its a forum markup command 
)
Correct:
< schematicView>
< p svgId="connector0pin" layer="schematic" terminalId="connector0terminal"/>
< /schematicView>
instead of (missing the terminalid definition)
< schematicView>
< p svgId="connector1pin" layer="schematic"/>
< /schematicView>the lack of the terminal definition is what is causing the middle of the pin to be used. I'm not sure whats going on with breadboard, the usual answer would be translates but I don't see any in the svg file. I usually find it useful (if time consuming) to ungroup everything as Inkscape at least then seems to undo all the translates (most of the time anyway) and then everything is to scale and you can move things to the exact coordinates you want. At the end of the editing I do an edit select all and then group and name the resulting group breadboard. Don't know if that will help here though. I copy / pasted a standard 8 pin .1 header over top of the connector in breadboard here with Inkscape and the new one looks to be correctly scaled (its offset from the grid because the grid is orienting on one of the pins probably connector0) so it doesn't look like a translate problem (at least not to Inkscape).
mojo_1.fzpz (74.2 KB)
So I don't exactly know what to suggest.
Peter