I gotta say this: Proofread, Proofread, Proofread. Usually when there is bad spelling and other technical errors the story in question isn't worth much attention, but this is one of those frustrating cases where grammar and other technical mistakes are the biggest strike against an otherwise interesting story.
I liked the slow start, although it could have been done better- It was a little too dry. But I really liked that the characters and their relationship were established before the transformation started. What's even better is that once the transformations did begin, you went straight into it, and didn't continue to drag out some confusing plot.
I also really liked the increasingly upbeat tone, and the happy ending. I'm all about willing transformations and minimum of mind invasion.
After the lack of proofreading, the second weakest aspect for me was the scarcity of physical descriptions during the transformations. The girlfriend's transformation, especially, is described almost entirely in the epilogue. As for the guy, you focused on the breasts to the point of excluding much of the rest of the body. The name of this site notwithstanding, there's more to the female body than the nice bits up front.
A tip on writing Female-to-Male transformations for a heterosexual male audience: a lot of authors get hung up on this because they think the end point of every transformation has to be physically desirable to the readers, and so when the story calls for FtM they either get confused and just hurry past it, or create a male slut. Don't do this. Instead of trying to write FtM as resulting in another object of sexual attraction, turn your girls into guys that male readers can identify with *as guys*: the sort of guys that guys actually think are cool, that they might like to be friends with in real life- the sort of male characters who are the protagonists of more typical fiction. You will end up with a much more useful character, instead of the typical FtM who just gets rapidly written out of the story.
