I have already found a solution where three of the blocks are the same, and I have proved that where five or six blocks are the same then the remaining blocks are forced, but I am having trouble showing the case of |$A\cap B$|= 4 either way.
I am guessing that $|A\cap B|$ can't be equal to 4, but am not sure where to start on my proof.
Any advice would be greatly appreciated.
Your guess is right. Up to isomorphism, there are only two possible configurations for the four blocks. If three blocks meet at a common point, the partial Steiner system is isomorphic to $\{123,\ 145,\ 167,\ 246\};$ otherwise it's isomorphic to $\{124,\ 136,\ 235,\ 456\}.$ In either case, the remaining three blocks are determined.