Dude, the subframe etc will not fit... they had a frame change in 1999. Why would you want to go back in time with the look of your ride?
For the piston clearance, if you're using a wooden dowel to hammer the piston out, and don't see there's a serious problem, you really should stand back and let someone else tackle the engine...
With the spacer, no, again, models were changed in 2003, different width swing arm.
You can cross reference these parts through any online Kawasaki Fische.