Not actual theories just bits of information that I'm hoping will lead somewhere.

Things like:

The fourth doctor's scarf being in Clara's house.
and the book the boy was reading being written by Amy.
Clara using the word Pond to get the Doctors attention.
a women (river?) giving Clara the doctors number.

My thought is that the doctor has tried to remove all memory of himself from the universe and somehow (via River or the universe or something) knowledge of him is manifesting as Clara.

Like I said proto-theory - not enough evidence yet for an actual one.