does a kawasaki zx9r 2000/2001 e1/e2 gearbox, bolt straight into a c1?

What is wrong with your gearbox.
I bought a 2007 zx10r last year with a know gearbox fault. A quick search on the Bay, and I found a full 2008 transmission internals in fantastic condition, and the price was right. That might have something to do with that they where in the US of A.
Anyway, the 2007 and the 2008 are slightly different engines, but the box internals still fitted.
I have looked on Ebay and the yanks have some replacement internals for your engine at good prices. Might be worth the punt.
Brad