I think that Jenna has some weird obsession with getting close to Emily, like first she brought in Shana and then Sydney and both of them joined the swim team. This is not really a theory, but it might be evidence that Jenna/Emily have a history before the show which I've seen is one of your theories!
Imagine if the Jenna/Alison war was partly sparked by Alison catching Emily with Jenna. So many things since then would suddenly look different. I doubt they’d go with that though.
But yeah, the Sharks really is a hotbed of intrigue. I’m wondering now if we can discount Shana’s claim that she had no idea about Emily when she got together with Paige, given that it appears she and Jenna knew each other around this time. Makes it all a bit complicated though.
Finally, I can’t talk about all this without mentioning how annoyed I still am that they killed off Shana. Urgh.