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I rebuilt my engine in 2006, and decided to do a bearing and piston ring refresh this month. I bought the same parts, from the same supplier both times, but I have no crank end play, and the motor gets stiff as I tighten up the gland nut. The end play shims were a little burnt looking when I took them out, so I assume they were tight in 2006 also. A friend suggests that I have the flywheel surface machined off .020 where the shim contacts the flywheel. If not, I will only be able to use one shim instead of three, and I know the three shims help act as a bearing when the clutch is depressed.
The case was align bored in 2006 and thrust cut. I have the thrust cut main bearings, as I should have. I could disassemble the engine and sand some off the thrust side of the bearing, but would rather not disassemble.
My three shims are .010 of an inch each.
What do you think?

If the crank/flywheel is still 4-dowelled, you could try simply adding the metal gasket between them which was used on the pre-mid`66 non-O-ring motors - that's good for an additional ~.012" endplay and there's really no downside on a stocker. The paper gasket's adds ~.008". Although I've never done it, you could probably get away with stacking two of them if you had to, but my gut feeling is that it would be better to stick with one and use just 2 shims. Porsches used a single shim for years, which kinda blows away the "three-and-only-three-shims" dogma. When you think about it, under the pressure of clutch pedal application the oil cushion between the shims gets pretty-much squeezed out (making the stack essentially a single shim). The real reason for using three shims was to reduce the number of parts which had to be produced and stocked to cover every eventuality.