It looks like you used an Adafruit part for the barrel jack, so your best bet may be to order that exact barrel jack from adafuit (I didn’t think to look at the jack part when I looked over the board.) I’d expect this jack will fit the holes in the part (as it is the product the part is for):
There is a variant in core parts from Sparkfun that has slots but note the warnings that it is experimental and the one with holes is the proven part. If you want to try the slot version, you should check with your board house if the gerber suits them. I remember a forum post where someone was trying to get slots and I think the conclusion was the Fritzing can’t easily do it.
Yes most of the Voltage regulators have pins that get larger near the case so there is space between the part and the board when automatically assembled by machine. There is a post from Old_Grey here with a laying flat version. I think this part originally had a translate in copper0 (that I figured out much later), and I don’t know if it ever got fixed. If you want to use this part, post and I’ll have a look over it to make sure it is correct.
While it didn’t come out as intended, I think it should probably work fine. All the isolated logic ground has been subsumed in to the ground fill, but even if not as intended, it looks like it should still work. The one non ground trace on the bottom looks to have been isolated correctly so it should work fine.
Peter