Now that Motorrad is a member of this site I can say that he is the member of the other site (KXRIDERS) where we started working on this issue.
It's great that Motorrad had this Digitron to point out the problem in the first place.
So here is the deal.
Check out the clearance between the impeller and the cover.
In this example I am using a Athena water pump gasket that measures .021"

- KX500 WATER PUMP IMPELLER CLEARANCE.JPG (37.09 KiB) Viewed 36820 times
So, depending on how you want to measure the clearance we need to shim the impeller approximately .080-.085" to take up the space.

- KX500 WATER PUMP IMPELLER CLEARANCE 2.JPG (38.81 KiB) Viewed 36820 times
With the correct amount of spacers you can get the impeller where it barely touches with no gasket.

- KX500 WATER PUMP IMPELLER CLEARANCE 5.JPG (42.28 KiB) Viewed 36745 times
Then, remove the cover, install your gasket, replace the cover, torque the bolts down and spin the drive gear on the back.
It should spin with no scraping and since most gaskets I have measured are the correct thickness range, you should now have the correct clearance.

- KX500 WATER PUMP IMPELLER CLEARANCE 6.JPG (32.93 KiB) Viewed 36745 times
Incidentally, yes I ruined a perfectly good cover to do this.
I do have the other half if someone want's it for the cost of postage

If bikes are for kids I'll never grow up.