I am just finishing off an R6k.
This is just stating the obvious really, but here goes anyway.
I have just pretty much ASSUMED that the only differences are:
1) The rims. I did discover that the bolts used to hold the front brake rotors differ.
2) The front fork internals and top screw and stanchion. (or to put it another way; only the fork legs are common to both R5k and R6k)
3) The rear shock.
4) The bits associated with the dry clutch.
5) The fairing livery.

Maybe this list is a bit vague,(especially 4) but I am not aware of any other differences.
Remember what they say about making assumptions!

If anyone knows of any other differences please let us all know.