Wow, thanks guys! Now I remember why I like this place. I ask a question and so many people are willing to help.
In fact, a few yrs ago I posted here asking if someone could go to the NJ DMV with me for my riding test. (in NJ, you can't ride alone on a learner's permit). TonyT607 jumped to the call and helped me out. He's a great guy and fun to ride with.
Ok, back to the valves. To answer some questions:

Yes, the engine was cold when I did the valves. In fact, I hadn't started it for a few days prior to working on them.

Yes, I am Mormon but I only have 2 wives. One is my current wife and one is my ex-wife. I have no plans to change the status of either.

About the TDC thing (and 180 degree rotation), I think I did it right. For each cylinder, I made sure that the "OT" mark was in the center of the window. I also checked that there was a little bit of play in the rocker arms for both intake and exhaust valves while at TDC. After doing one cylinder, I rotated the back wheel in the forward direction until I found the "OT" mark again. Then I hopped over to the other side and adjusted those valves.

Yes, I took out the spark plugs first. I will take Cyclerob's advice and read the OVAD document carefully and do this again (without removing the plugs).

One strange thing - I changed the oil today and now the tapping isn't as loud. It's still there but now I hear what mostly sounds like the timing chains moving through the heads. I wish I knew exactly what sounds are "ok" and which ones are not ok. I guess that's part of owning an 1150R -- seems like the most frequent question is "what's that noise?"
Thanks again guys. If any of you are ever out in Utah let me know. I'm sure you would love to ride through our canyons and red rock country.
John