The cam caps are labeled I1 I2 E1 E2 etc. and I placed each one carefully in order when I took them off, so I'm quite certain I didn't get them on in the wrong order. I have ordered more shims so I will see what happens once I receive the new shims and put everything back together.
I only moved the cams far enough out of the way to remove the lifters so I really don't think I could have bent a cam. I only removed the lifters where shims were being replaced. So I'm certain I didn't mix up the lifters/buckets. When I took the lifter off in order to take the shim out, I put the lifter right back in so that any mix ups were impossible.
So I'm not sure WTF happened. Once I get the new shims, I won't be ordering any more. All of my clearance readings have been .001 on the tight side, so I should be able to sand down any additional shims. Once I get the new shims, I'll see what transpires next.
I also replaced the CCT, but I don't see how that could have effected the clearances.
Initially I only had one intake (cyl. #3) that was .001 too tight and one exhaust that was .001 too tight (cyl. #4). Now I have both intakes on cyl#1 and cyl#2 .001 too tight and one exhaust on cal #3 .001 too tight. So including the original shims (two) this makes a total of seven shim replacements which seems to be unheard of for a first valve check/adjust with 26K miles.
In addition, I spun the crank around at least 3 times and made the original measurements multiple times to validate the measurements and ensure I got consistent results before pulling the cams and lifters.
Once I put the cam caps back on, I did the same thing by spinning the crank around multiple times and made the measurements multiple times. As stated before, once I get the new shims back in, hopefully I'll get consistent results this time. Maybe it was the Jameson's Irish Whiskey the night before?