After thinking about it, Jeff did find it kind of cute, but knew there could be a few issues. Emily still remembers being, and acts like, a girl. The change 'down there' could make a difference, so while Jeff wanted to keep Emily as his brother, he decided to compromise on it. He ran back to the Chronivac, wanting to put a sort of 'In-between' on what Emily remembers, and what Jeff wants Emily to be.
Jeff put some specifications for an extra change; Emily would still act mostly like a girl, but lean a bit towards a neutral personality. Emily would be a hermaphrodite, having the vagina he remembers having his whole life alongside the penis, with both functioning for their intended purposes.
Emily would identify as a boy, as Jeff wanted to keep that part, but still be fine with female pronouns. He'd still use the girls bathroom, since everyone knows of him as a girl, and his name would remain the same.
Jeff was happy with this; He'd still have the little brother he'd wanted Emily to be, but Emily would adjust to his new life a lot more easily. He put in the change, and ran down to see the changes visualize.
Externally, it was near impossible to notice much change; All Jeff could see was his brother's hair lengthen out, half way to what it was before the Chronivac. What he couldn't see was the change in Emily's pants, as all of the female parts were restored around the male ones.
A slight bit of Emily's height was taken away again, just enough to be noticeable but not actually change the 3'8" that Emily was presently set at.
As Jeff watched, Emily didn't seem to really notice. He guessed it'd be a bit, since Emily never went feeling around in her privates before, at least to his knowledge; He was expecting it to be a while for it to be seen, especially by him...