John, excellent pictures and post.

I went through the same process 2 years ago (had an overheat)and discovered as you have that the hushers (I call them cushers) close down the valve clearance making it difficult if not impossible to measure with any confidence. Those hushers will break in and collapse somewhat during the first few minutes of running but in the meantime you may find that the engine runs really rough. That was my experience and I concluded that it was the hushers not allowing valves to fully close. After a few thousand miles I went back to check valve clearances and of course it was then quite easy to perform.

My theory of the hushers is that they act as suction cup to stop the buckets from rising away from the valve stems from inertia and thereby preventing buckets from slamming down on the stem next time the cam lobe comes around.