OK, I've looked at your latest pcb, the problem is that the pads in the svg are set as paths. To work they need to be circles with a set diameter and stroke-width in Inkscape .078 " diameter with 20 (I think thousandths of an inch) stroke width. Those values then get sent to a python script which generates the pad at .078 inchs and sets the drill size to .038 (by subtracting 2*stroke-width from the diameter). When I use file->export->for production->extended gerber to create the gerber files that would be sent to the fab house to make the board, most of the pads don't appear (although some do) and none of the drill holes make it. Inkscape really doesn't like your pcb svg, it shows the entire top row of the top 2 row connector missing and a few pads in the next row missing, only 4 out of 6 of the side connector and only 8 of the 50 pads on the bottom. As an example here is pin 50 (the top left dual connector marked raw just below the square ground) from your pcb svg file:
<path d="M25.2,16.09A1.91,1.91,0,1,1,23.29,18a1.91,1.91,0,0,1,1.91-1.91m0-.25A2.16,2.16,0,1,0,27.36,18a2.16,2.16,0,0,0-2.16-2.16Z" transform="translate(0 0)"/>
here is pin51 from my working pcb svg posted as Embedded Micro Mojo v4.fzpz:
(note it is desirable to get rid of the transform if you can, I usually struggle with it because I don't understand why Inkscape does it)
From this fritzing takes the r="29" and the stroke-width:20 and the cx and cy values and the script then generates the gerber file from those values (ending up with a .038 drill hole in a .078 diameter pad). Fritzing seems to be dealing with the paths better than Inkscape (in that pcb view is showing the correct pads but without the red connector dots, presumably because it is looking for an id attribute that doesn't exist in your file) but can't determine a hole size due to no radius or stroke width. If you can get a construct like my pin 51 in place of all your connector paths (in the same x y coordinates) that should work.