I thought that Brian only wanted to reunite the worlds so that he could go home? So if he's already been back to Stark via Shifting, or any other means, surely he would have just stayed there rather than carry on with the whole reunification plan.
There is some (deliberate?) ambiguity as to Brian's motivations, but examining his dialogue, I agree with Pawlo_86 that his main reason for wanting to destroy magic was to save Stark from the troubles that the reunification of science and magic would unavoidably bring upon them. That was his initial belief at least, getting home was just a bonus, though that probably ended up being his main drive. I actually believe (though there is only a few pieces evidence for this) that this was actually the reason behind his journey to Arcadia, he wasn't just simply a curious traveller. This is mostly implied in his journal and during the balcony conversation with the Undreaming. Unfortunately, it's kind of impossible to grasp the true nature of his (and Cortez's) initial plan, I have a hard time beleieving that he wanted to initiate genocide in Arcadia, that probably came because of his corruption through the Undreaming, But some aspect of "saving Stark from magic" was always there in his mind, I believe.
With that said, I don't think that he was a Shifter or that he has ever been back to Stark. There was definitely a longing in him to get home, which wouldn't been right if could do that all along. The question of how Helena and Brian communicated, well, that's a mystery. I'm not even certain who approached whom. My guess would be that Brian reached out to Helena and not the other way around. ("You were just a puppet, nothing more."), but I guess it's also possible that Helena was the first to communcate with Arcadia, and Brian just took advantage of the situation. I like the theory that Gilmore was somehow involved in it though.
Let's hope that Ragnar's comments mean that we'll still learn something about this later, be it through the Complete Edition or somehow else.