Valve Clearance 2000 yz426

I'll try to keep this brief. I'm the 2nd owner of a very well maintained 2000 yz426. I bought the bike in 2002 and quickly did the exhaust cam upgrade in 2003. Every 40 hrs. (or so), I've checked my valve clearance and they've always been in spec. Checked clearance last week and measurements were way off- .06 for intake and .13 for exhaust. I picked up new valve shims from my dealer that should put my clearances back in spec. Put the new shims in and my clearances are still off. Much closer, but still off- .13 intake and .22 exhaust. I noticed when I put the shims in that they would sit below what I'll call the valve pit. I didn't think anything of it because the cups have a little nipple in it, and this is what rides on the shim. I'm not sure what my next step should be. I thought I could run it for a brief time and hope the valve parts mesh together giving me the propper clearances, and I've thought I should order new shims. The problem w/ the shims idea is that these shims should have put me on the high side of the specs and I was very careful when I determined what shims I should get. I used the charts and the calculation method for help. Could the nipple in the cups be too worn? Any ideas?

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