If you can tell me what you need I can fix up the parts and maybe figure out how to put them in to a pull request (I'm just learning git as well.
I can (and I think on the Zero did)) fix all of that, but it will break all existing sketches that use these parts and I don't know how that is dealt with (being relatively new to Fritzing). The issue that I asked about and don't have an answer to is what is the accepted way of making a change that will break existing parts? If I remember correctly the PIs are one of the parts that don't start at pin 0 and more importantly don't have contiguous pin numbers (which breaks the hover over the pin to display the labels function). 1 in as it should be) and I changed the schematic around so that it matches breadboard and posted it in the forums.
I have done a corrected version of the Zero (which has the pcb header the wrong size, maybe 2mm but not. Actually all of the PI parts are a mess, more internally than external.