Working on a few of these recently (and looking at a few for friends to buy or sell) I decided to list the changes I could find. More than I thought, for sure, but some of them are really small stuff.
Most of these are harvested from the fiche but the context is of course lacking. Could you please send me (PM or post it here) any information you have pertaining to these and other changes? Could make a nice buyer's reference at some point.
ZB50001 through ZB50004, pre-production.
ZB50005 through ZB50016, early production in 04/1998
Production started 6/1998 with ZB50017
Very early models had plastic inserts in the fork tubes, to displace oil volume. These were deleted by MY2000.
08/1998 clutch bleed screw changed
03/1999 extra screw added to switches (in mirror hole)
04/1999 fuel distributor hose protection added (recall 01V-272)
03/2000 harness change
09/2000 license plate light & subharness
No production (US at least) 11/2000 to 05/2001
Production resumed 05/2001 (ZB52122) with:
EVO brakes w/Integral ABS (15mm rear MC, new brake lines, calipers, more)
new seat and subframe
08/2002 EVO transmission
09/2002 iABS rear brake lines changed, different modulator, different switches, clear turn signals
10/2002 iABS rear caliper & pad change to sintered
12/2002 Twin Spark, oil pressure switch,
06/2003 iABS front calipers and pads changed
07/2003 ELAST alternator belt & pulley
12/2004 throttle cable change
'04 BCR got different instruments, forks, sidestand, special brake hoses (non-ABS only)
Sport suspension changed in 09/2000, affected rear shock and torque arm
The ECU chip changed form/package/pins but prolly not content early on. While this is a component internal to a stock part, it does matter to modifiers, people who buy bikes that were re-chipped (BBP, FIM, muffler chips, etc.), and when chips break.
It is rumored that some ECU software changes also were introduced besides the dual-plug changes. But since nobody has reverse engineered the ECU for timing and injection (or least, done so and then talked about it), not sure.
The old seat and the new subframe and the reverse can be finagled to work; after-market seats can be designed to fit both.