Well, I can't really talk about the process, but I can talk about the issues that one of my friends encountered when he transfered.
First of all, this guy is top notch. Good grades, great PT scores, and the such. He transfered as a Junior and was thrown into the supply shop. When it came time for rated boards, it was obvious he wasn't going to get a pilot slot, because all he had done was run the supply shop. The Commander had no clue what kind of person he was.
Well he ended up getting a Nav slot and then he was given the MSG. The dude rocked it like no one else before and then was begged by the CoC to take the position of Vice WG/CC to keep things running. He shot up in class ranking from around 25 to 3 in a period of 3 semesters. Fortunately due to some shrewed drug deals, our CC got him bumped up to strike nav, but everyone in the class realized that he was given the short stick due to his transfer.
Long story, but hopefully you get the point. Not saying this will happen to you or anyone else for that matter, but it happened to him and he was a hell of a guy. But I understand the need to go some place where you are happy and where you want to be.