Hi LAX - tell us when your story is done - we would like to read it!
I promise you I will post links to any stories I might see that matches your requirements! I am always looking for stories that have Tok'ra in them - any Tok'ra, even OC's so hopefully I will come across such a story eventually. I agree with you that most authors unfortunately follows O'Neill's lead in disliking the Tok'ra. It is really too bad, as they are fascinating characters with their duality.
Some of my favourite stories are GEN about the backgrounds of the characters - like why did Egeria become Tok'ra, or how did Martouf become host to Lantash. I also like stories about the Tok'ra and there missions before they met SGC. Stories about the Goa'uld and their society is fascinating as well. So if anyone sees such stories, then please post a link to them here!
As for ship - I will read almost any ship-story as long as at least one (sorry, two - host & symbiote ) of the participants is Tok'ra. My favourite ship is Sam/Martouf/Lantash - partly because they seem to have such great chemistry, partly because the problems/extra dimension of the remnant of Jolinar fascinates me. I would however prefer Jolinar to live, though - she is one of my favourite Tok'ra, second only to Martouf/Lantash.