The easy way to do this is to increase the radius of the pads with xml editor in Inkscape. If you do pretty much anything else the x/y coords of the pad will move and cause problems. What I did was copy / paste a pad from a header (as the headers have the .038 hole size you need for .1 pins) in to the pcb svg drawing, then copy the radius from the header pad in to all the current pads using xml editor. Then copy the entire style command from the header in to the pad. Note there is an Inkscape bug in 0.92.2 that it loses the change when you change an attribute which it converts to a style (for example if stroke-width is separate and you change it from 10 to 20, when you set it Inkscape will convert it from in line to a style command but retain the original value of 10). So what I do is select an attribute (with no changes), set it (which converts to style) then replace the entire style with what I want and set that. There are tutorials on parts creation and I highly encourage everyone to learn parts making, it just has a large learning curve 
. A number of us are happy to help if you have problems as the more people making parts the better. Yes the spacing is the one between the rows as you have discovered. If you want breadboard and schematic for your part as well it would be fairly easy to adapt either one in core by replacing their copy of the pcb svg with yours. You would probably need to change the connector numbering to match that used but the ones in core though. Here are pointers to the parts making tutorials:
Peter