OK there were a number of problems. It looks like you were confusing the onion module and the doc (which is what you are trying to make). The module has 32 pins and the doc only has 30 (also there is a documentation error on the Onion site at
at "The Hardware"
it shows a 32 pin connector (with only 30 lines labeled). where the doc really only has a 30 pin connector (seeing that I started with a 32 pin connector 
). In any case lets start with what I did to fix breadboard:
Scaled the omega to 26.40 * 42.70mm (according to mechanical drawing) as is it was too large. Copied in from another svg 2 15 pin single headers (because duals are currently broken) via a cut and paste in Inkscape. Added and positioned (according to the mecahnical document on the Onion web site) the dual 30 pin connector (2 single 15s grouped) after deleting the 40 pin connector that didn't have any connections attached. Then changed the connector pin designations to match what they should be for a dual (i.e.
pin 1 3 5 ... 29
pin 0 2 4 ... 28
(note: need to do this in schematic and pcb as well). Grouped then scaled and corrected the lettering on the labels and moved them to match the connector holes (using the connector documentation from the onion web site). Select all group set group id to breadboard Select all resize page to drawing and breadboard is done.
Schematic
Rather than add connectors to yours, I created a part in Fritzing from a generic ic with pins set to 30, saved it as a new part, exported the part, unzipped the fzpz and swiped the schematic svg to copy in to yours. That gave me the correct number and configuration of terminals. Then I renumbered them to match breadboard and made the rectangle larger and added the pin labels from the data on the onion site. First I used xml editor to set the stroke and height of all the terminals from 0 0 to 10 10 (making a 10 thou by 10 thou rectangle as the terminal) with 0s Inkscape will not select or move the terminals. With a 10 thou rectangle it wll. At the end of it all again edit->select all and group setting the id to schematic this time. Then select all and resize document to page and schematic is done.
PCB:
As noted your copy of PCB had the onion module which isn't what is needed here. So in Fritzing selected a connector, changed it to 30 pin double row (which doesn't work in breadboard view but does in pcb), edited saved and exported the part and then swiped the pcb svg to use for the onion. To start with it only has the dual row connector, so yet again renumber the pins to match breadboard then from the io doc mechanical drawings add the necessary lines in the correct places in silkscreen layer to produce an outline of the edges of the board. Save it and pcb is done.
fpz file:
Fixed up the metadata to remove references to the pi zero (which I assume you cloned this from) and add a description and more tags. Then moving on to the connectors, changed the names and descriptions to match those in the documentation on the onion site. I also deleted a number of extra connections possibly left over from the pi zero (which has 40 pins). Fixed up the bus pins to have the appropriate and appropriate number of members. Rezipped the resulting files in to an fzpz and loaded it to fritzing to test. The result is here:
onion_fixed.fzz (136.7 KB)
which is a sketch with the new part available to be exported by right clicking on it in temp and selecting export part. As you see all the pins make correct and correctly placed connections to the two 15 pin connectors used for testing. As well the pcb has paths on both sides of the copper and I exported the gerbers and checked that the drill sizes are correct and the silkscreen looks correct when exported. You should check all the pin labels go where you think they should in case the problem is that you have a different version than that described on the onion web site, but I think the problem was confusion between the module pinouts and those of the io doc. If you have questions feel free to ask.
Peter