Checking and adjusting Valve Clearances

A bad sound made by the engine has led me to check the valve clearances.  Equipped with the "big blue" "Honda 360/400/600 Sedan and Van"  manual, the Haynes manual, and a new set of feeler guages, I took a look. 

I used a 17mm wrench to turn the crankshaft and move the camshaft. 
After moving the camshaft as described in the manuals, I found that the #1 and #2 valves (looking left to right) were right at .004", the #3 was at less than .002, and the #4 was at .005.  I assumed that the number 3 was the trouble, though all the literature says that a too-LARGE clearance causes the symptom, not too small.  anyway with some trial and error I got it to .0035.  Close enough (?)

Unfortunately this didn't fix the problem of the "bad sound".  Although I thought the engine may have sounded better when I started it up after doing the adjustments, after a few minutes it was back to it's noisy self.  I will have to go back and inspect again.  If nothing has moved then I am at a loss about the sound.

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Oh, and to make matters worse, the #3 had a bit of the aluminum case bent down onto it's spring.  I gently tapped it straight after taking this picture... . 

Here is what a good one looks like - it is right at .004 clearance...

Here is the "big blue" manual's page on this topic...