So after finding the Moth Priest, I freed him and he immediately attacked me. I may have indirectly dealt some sort of damage to him from my lightning cloak or a stray lightning bolt/chain lightning.

Anyway, after nearly killing him I was able to speak to him and he told me he would meet me at the dawnguard fortress.

Upon arrival he was immediately attacked and brought to his knees by everybody in the fortress, again I was able to speak to him and get him to read the elder scroll in this state. However after having read it I can no longer speak to him and after healing him he is again attacked and brought to his knees. I can not go any further int he dawnguard storyline until I find a way to fix this.

Any suggestions?

Have you got a close save game to were you freed him?
At first i thought my game was bugged as just after i freed him he attacked me until he had 1/10th of his health. this part was suppose to happen, although the second part which you described didn't happen with me.