Breadboard looks good now, I'll have a poke at schematic and pcb and see if I can do something about it in Inkscapes (which hopefully may translate to Illistrator). You have done very well for a first part as part creation is a complex process. The hole size for pcb is a combination of the radius of the circle and the stroke width. In inkscape the standard stroke width is 20 (I think px) and the diameter of the circle needs to be hole size + 2*stroke-width so for a .038 hole in Inkscape with a stroke-width of 20 the diameter of the pad needs to be .078 in. On your initial part the radius was something like 1.5...(which I've seen before with translates being present) in which case I usually copy and paste a correct pad from another drawing in, move it to the correct group (to get the transforms to take) and then copy the radius and diameter numbers from the xml display and use that to set the other pad values. If you can't get pcb correct it isn't a big problem, most people are probably going to use the part as you are to document things from breadboard view.
Peter