Welcome to Bike Forums.

You have already identified problem one, the recessed nut on the rear. Is this problem present on the front also?

The second issue you might already be aware of - did you check to see if the Sora calipers reach the wheel rim? Mafacs have a pretty long reach, as I recall. Not sure about the Sora calipers, though.

If you really want to use the Sora calipers, you might try finding an orphan front caliper and use the mounting bolt from that on the rear. All that said...

I am a fan of the Mafacs. Not only do they work really good, if set-up properly but they all but scream "vintage" to me...