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Actually, you will want to swap out the whole wiring harness with an S-harness if you want to avoid headaches. The plugs are different between the S and naked gauges, and the S model used a sub-harness for the gauges and headlights, etc. The main harness has different connections too. Sometimes (from Ebay) the S harness will come with the sub-harness included (I was lucky to get this), but sometimes it won't. Its hard to tell when looking at small auction photos.

You could also just use the fairings/headlight and keep the naked gauges, but you would have to custom rig something to mount them. You would have to do some minor splices to get a 2nd headlight connector. I have some spares if you need them.

Unless you keep the naked model handlebars, you will also need S-model throttle cables, clutch cable, a S top clamp, clipons, bar ends. There may be other minor parts too.

BTW, my 99 bike has gone through the full conversion to an S-bike. The previous owner took it half way there (fairing stay, fairings, headlights, windscreen), but he kept the naked gauges and had non-stock mirrors that sucked. When I bought it, I did the rest of the job (S harness, S gauges, S-dash cover, S-mirrors, S mirror inner covers, S-cables, different clipons) to make it look stock.

If you are interested, the whole process is documented (starting with the previous owner through the work I've done)
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