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I just picked up a 1994 KDX 200, and the clutch has the last plate lined up in the fingers of the basket, like this:
In all my other KDXs, all of the plates have been lined up, like this:
Which way should the plates be oriented?

The 94 is correct, all your others are not. From the service manual "Place the last drive plate on the outer tangs of the clutch hub"

That second clutch has some serious notching going on there that will need to be addressed.

Here's a 1995+ version on eBay. It may have never been apart.

I think bufftester is correct.

https://www.ebay.com/itm/363516439923?f ... 7675.l2557

Why the last friction disc is was offset to the others from the factory makes no sense and makes no mechanical difference to clutch operation. Install it however you wish.

That last plate being offset is technically the factory installation method, however I don't believe it matters. Maybe has something to do with the judder springs? Most aftermarket baskets don't even have that provision.

Look up "notched clutch basket".