Jaytee, forgive my laziness. I just reread your initial post.
The bike started fine but the idle was high so after some minor adjustments it idled beautifully at 1100 rpm (really smooth compared to my 74 CB750).
Congrats, nothing abnormal here.
After about 10 minutes running I noticed that cylinder No. 1 was running cooler than the others - the header was hot (ish) but the muffler was a lot cooler than the others.
Ignore the muffler. Is the no.1 header much hotter than the rest? BTW, you never will have them show the same temperature.
Pulled the plug and it was a tan color.
Good, however usually the CB500s run quite rich at idle.
Note that I haven't run it on the road yet as it is not fully assembled.
Let's wait for that then.
I checked the float level with the clear tube method and it was at 5mm below the seam so a couple of mm out. Would this be enough to make it run cooler ?
Not likely. You'd expect the contrary. Also I would like to stress that you haven't checked the float level but rather the
fuel level. Do verify fuel flow. Usually the float itself meters OK for decades and decades, as long as it is not tampered with, which seems to be a hobby in this forum. I suspect the presentation in the Clymer manual on this has to do with it.
Other thoughts are to check the valve clearance on this cylinder and balance the carbs (it revs cleanly and idles really well so they don't appear to be badly out of balance)
Maybe, there's not much of a problem and you're overthinking it. I mean, it idles fine and you have not been on the road with it. So, what do we know?