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Getting a bunch of offers to replace my engine. Chime in if you know what different years of engines will mount to a 2006 frame.
 

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I'm pretty sure you can transfer the left case cover and associated charging components from your old engine (2006) to your new engine (2000). I'm not sure if the rotating components (magneto) are different, probably are, but I don't see why they couldn't be transferred as well. I'll see what I can find out.

Edit:
2006 Magneto 5BT-85550-01-00
2000
Magneto 2YG-81410-M0-00

Looking at the tw200 main manual and the 01 and newer supplement it sure looks like the magnetos could be switched, but I guess I can't say for sure. Maybe someone who has done it will speak up.
 

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I agree with B-dub. You should be able to transfer your left cover and electrics as well as the magneto to the other engine. That way you can have the updated system and use your current cdi. The only other thing that is different on a pre 2001 engine is it has a manually adjusted cam chain tensioner, unlike the automatic one you currently have. I wouldn't let that stop me though, they are very easy to adjust. I adjust mine at the same time I do the valves.
 
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