If they're noisy they're most likely still a bit loose. It's commonly believed they're too tight when quiet, but not necessarily so.
One of the tricks is to push down on the rocker to eliminate any oil film on the pushrod to lifter connections while feeling the gap.
Another is if the push rod will twirl (while feeler gauge installed) it's not too tight.
Something to consider is the low spot of the cam --- where is it exactly? If you've seen a cam, you'll remember that they're not all aligned with the peaks right in line? So using TDC as the place to adjust them is a guess that it's the lowest spot for them both. It's not real critical that you align the engine to exactly TDC. If you see it in the window it's good enough!
I set my valves at .004 and .008. Intakes don't need the clearance since they don't get as hot as the exhausts opening and closing the 'blast furnace door' all the time. One of the considerations in clearance is the larger it is, the longer the valve is on the seat transferring its heat to the head to dissapate.
Another thing to keep in mind is some people think that noisy valves is a good thing - but it isn't. What you're hearing is the rocker hammering the valve stem, wearing both. The rocker has a nice curve to it and once that's damaged it doesn't work as well.
Finally, the valves were probably quieter at the beginning of your ride because the oil was thicker (being cold) and cushioned the rockers more.
There's something magical about these bikes when they're running right, as you noticed. They uplift the soul.
But when they're not (and it doesn't take much) they feel like crap.

I frankly believe a lot of these bikes get sold or put in storage because of this phenomena. It can be as simple as needing the carbs synched or a mixture adjusment.