Yes the '85-'89 is analog ignition, two pick-up coils, the 1990-'07 is digital, one pick-up coil. Different rotor, I expect the stator too. Different wire harness, different ignition box to upgrade to the 1990-'07 ignition.
Don't forget about the oil filter & curved cross-brace for the frame.
If you're intending to back-swap to the early ignition components onto the new engine, yes, swap the new rotor off, add the old rotor, replace the straight front-of-frame brace w/the curved one for the spin-on oil filter. The old left front engine cover should swap right-on the 2000 engine. The old stator stays right where it is.
I expect Sean Morley will weigh-in on the driveshaft, or Captain Kyle.
That should get you back-on the road. Consider going to the newer wire harness (a used 1990-up should be cheap) and digital OEM ignition box, or an Ignitech from Sean Morley. The Ignitech is more tunable, it can control more bike functions, and is supposed to be less prone to issues from the use of COP's. There is also the DYNA ignition box, the old version and the new version.
