Hi BigJalle,
let's get things sorted - I'll start with your pics first:
- 03 NR1: 2003 SEM CDI
- CDI 06: CDI for Kokusan stator
- 06 NR1: 2006 ignition coil
- 03 NR: 2003 SEM rotor & stator
- 06 NR2: Kokusan rotor & stator
- 06 NR3: Kokusan rotor & stator
When you'll swap engines from 2006 to 2003, you better replace all units - that will save you lot's of machining work, making an 06 rotor/stator fit an 03 engine. So put the 2003 engine and the 2003 SEM CDI in your bike.
Remove the typical 2006 parts:
- 2006 Ignition coil
- 2006 CDI
- 2006 TPS from your carburettor, the 2003 one comes with a Dellorto Carb and the 2003 CDI doesn't work with TPS modules...
When you put the 2003 engine in your 2006 frame you need to connect the 2003 SEM stator to 2003 CDI:
- [stator] red --> [CDI] red
- [stator] green --> [CDI] green
- [stator] black --> [CDI] black
So far, 3 cables sorted. On your SEM stator there should be 3 cables left: 2 yellow and one blue.
- [stator] blue (ground, mass) --> put it were the other ground wires go (e.g. bike frame)
- [stator] yellow --> yellow cable on your 2006 harness, which connects the light switch with the headlight and the rear light
- [stator] yellow --> white cable on your 2006 harness, which connects the regulator-rectifier to load the batterie etc.
The stator cable are all connected now. From your 2003 CDI there are a few cables left to connect:
- [cdi] gray --> you can leave that one open. On a 2003 it connects to your "High/Low Ignition Curve" switch, which I guess is not available for 2004/older models. If you like, you can add on (closing circuit to ground)... but it doesn't change a lot....
- [cdi] orange --> yellow/blue wire (stop/kill switch), connected with your key switch (your 2006 harness)
- [cdi] white --> yellow/red from your 2006 start button (connects to regulator/rectifier, fan, flasher system/blink relay, speedometer)
- [cdi] black --> ground wire connection point, e.g. frame
Since I did this in my lunch break and never mixed a 2006 and a 2003 wiring harness before,
take all information carefully! No liabilities on those tips 
Anymay:
Always work carefully, cross check everything, voltage, amps... Check your connections and switch functions with a multimeter.
I don't know if the 2006 regulator/rectifier will work with SEM output. I guess it does, but it's not for sure. Also check your SEM stator first, before you swap anything. You measure the resistance in Ohm with your multimeter between the following wires:
- [SEM stator] black - red: 2900...3000 Ohms
- [SEM stator] black-green: 160...170 Ohm
If your measurements are out of range, your SEM is already fried. You can buy an aftermarket replacement at electrex (
Electrex World - Motorcycle electrical parts for Japanese, European & British bikes)
I attached a few pics, a 2005 workshop manual (wiring diagrams at page 127), and a 2003 wiring diagram. I hope I could help you a bit. Maybe somebody from this forum also has some input and knows better,
regards,
EDE
