Here's the breakdown guys for the 85-89 to 90-07 Harness Swap Requirements:
CDI (85-89US model has Gold Label vs 90-07 has Silver Label.)
Pickup Coil (85-89 has double vs 90-07 has single)
Flywheel (85-89 has two long lobes vs 90-07 has multiple small lobes)
Gauge Cluster (will swap but 85-89 harness for fuel light is different then 90-07 so must swap that out of the harness at a minimum). All physical gauges will interchange.
Sidestand Switch (85-89 has larger 2 prong white connector vs 90-07 has smaller 2 pin blue connector)
Starter Relay (85-89 has single bullet connector vs 90-07 has 2 prong connector). They can be swapped but requires some wiring modification to work. A jumper has to be installed on the later model if used on the early model.
Turn Signal Relay (85-89 has 12ish? pin vs 90-07 5 pin connector)
Sidestand Relay (85-89 has blue capped housing vs 90-07 has all black housing)
Items that fit ALL years:
Headlight
Taillight
Signals (Front's are 3 wire and rears are 2 wire)
Speedo
Sending units for coolant temp and fan control
Vboost Black Control Box
Vboost Servo
Fuel Pump Relay
Low Fuel Sensor
Clutch/Brake Switches (including rear switch)
Neutral Switch
Oil Level Switch
Horn
Fan
Vacuum/Pressure Sensor
Coils/Wires
Fuel Pump
Sidestand Diode
Main Fuse Block (above battery)
Voltage Regulator
Stator
Starter (90ish and up have better starters - identify by smooth barrel on the body with no phillips screws).
Handlebar Switch Housings Right and Left
Ignition Switch
I think that's about all of the OEM stuff.
IF, you swap to the Ignitech that Gary (Dingy) has helped us get (and I try to stock) then you can use that unit to run on either harness type with only a program change and adapter cable change. It can be configured to run the COP (Coil Over Plug) conversion without resistors. It can also be used to directly control the vboost and eliminate the vboost black box (which is starting to go bad with the ages these bikes are getting). Not to mention all sorts of other accessories.