I agree with the piercing and corset idea, maybe not corseted to the extent of a wasp-waist (or other extreme deformation), but quite tight and ajusted tighter every day so as to cause some discomfort and a noticable change !
And then the scientist could remove her corset every now and again to examine the progress. (very hands-on)
Nipple rings would be good, and piercing other places too, and much attaching of chains and stretching. ::evil grin::
As for hair removal, I'm not too keen on the idea, because hairless bodies are too overused in stories. It's all very well individual people having hairless bits, but it's so cliched in stories and porn that I find it a bit numbing, I like variety (that's why I like japanese porn, it makes a change).
Maybe her pubic hair could be bleached and dyed an interesting shade, and cut oddly.
I like the idea of the man showing this girl off as his pet to his work colleagues while the modifications are underway.. Needless to say they give her a full body inspection and she is subjected to plenty of tests.
A bit of mild electrocution wouldn't go amiss either.
Sorry if I seem a bit short of ideas.