Zenos and Fandaniel's motivations and goals are naturally key to EW's main scenario so they'll be answered as you play through the MSQ (so anything I say will be big spoilers). I can say though that Zenos' body was posessed by Elidibus not Emet (Emet used clone bodies of Solus as a young man).

And Zenos's soul survived because of the Resonance procedure used on him in SB - it basically turned him into an Ascian in a way in that his soul could reside outside his body and return to it (or possess another).

Finally Zenos and Fannyboy used each other for their own ends, again the reasons for are revealed in EW so keep playing! It will be all explained in time.