Here is an excerpt of an E-mail exchange I had with a gentlemen in Hawaii that wanted to put a 2000 instrument cluster in his 98 R1. As it turns out we got it all to work. In addition, to what you see below, I believe we also had to wire into the oil level switch circuit, a relay for ‘logic inversion’, so that we could get the oil level switch to work.
As Scott has already suggested, and I concur, installing a 2001 harness in your ‘99’ will be a project you will probably be sorry you ever started….sorry.
Anyway, here is the excerpt…..
Wayne,
This is the way I interpret what's going on.
1) The green/black wire coming from the 2000 dash is the 'fan relay activation line'.
2) The green/yellow wire coming from the 1998 dash to the Ignitor Unit is the 'bad fuel level sensor' wire.
3) From review of the specifications for the 1998~99 temperature sender and the 2000, these sensors are totally electrically/functionally incompatible. The 2000 sensor will not work with a 98~99 dash and a 2000 dash will not work with a 1998~99 sensor. It appears that Yamaha decided to incorporate a speed sensor tach diagnostic for model year 2000. This then 'pushed' the responsibility of fuel level sensor diagnostic on to the dash. This action then 'frees-up' a spot in the dash connector where the 'bad fuel level sensor' wire (green/yellow) went. Yamaha then said 'If we use the temperature sender information for both indication and fan control, and use this 'open slot' for 'fan relay activation', we can save the cost of a thermo-switch, installation time, and some radiator configuration work, all for the cost of one fan relay! As I see it, they saved some money at the cost of some system redundancy in a 'safety critical' system. By having a separate sender and switch, if one fails, you still have the other to either indicate temperature trouble or control temperature. With this system, if the sensor fails, you lose both. Not good in my mind (the bean counters will always win a fight against lawyers in the corporate world).
Anyway, here is my recommendation Wayne.
1) Use the 2000 temperature sender. If the 1998 wire harness is not compatible with the 2000 sender, modify the 98 harness (add mating connector for 2000 sender).
2) Use the 1998 temperature switch. This will of course plug right into the 1998 harness.
3) Snip the green/yellow wire on the bike 'main harness' side of the dash connector. Connect one end of a 100 ohm resistor to snipped green/yellow wire coming from the main bike harness and connect the other end to chassis ground.
Sam