I had a very similar experience as the OP trying to re-install my distributor. It turned out that the O-ring I had was a little too thick and was preventing the distributor from dropping all the way in to the oil pump slot. I determined it was the O-ring because I was able to seat the distributor all the way into the oil pump slot with the O-ring removed, but when I replaced the O-ring, I was unable to seat the distributor all the way into the oil pump slot.
Two things that helped me to get the distributor seated all the way into the oil pump slot.
(1) I got a slightly smaller O ring (size 210 - 1/8" W x 3/4" ID x 1" OD)
(2) I followed the procedures outlined in the posts above to get the distributor seated all the way into the oil pump slot WITHOUT the O -ring installed. I then took note of the orientation of the rotor and removed the distributor. I then installed the O-ring on the distributor, and re-installed the distributor with the rotor in the same orientation as I had it installed when it was fully seated with no O-ring. At this point, I was left with the 3mm gap between the bottom of the distributor clamp and the block. However, because I knew the distributor shaft and the oil pump slot were aligned (from installation without the O-ring and noting the position of the rotor), I just pressed down on the distributor body with some oomph and the O-ring slipped in to the hole and the distributor fully seated into the bottom of the oil pump slot.
Hope this helps anyone else struggling with their distributor!