Basically, you can burp the coolant when ever you really want to, just keep an eye on the temps until you do it. If the engine starts to get hot rapidly, shut 'er down, cuz you may have an air bubble in the water pump. Most newer coolant systems are designed so this isn't such a concern, in that it doesn't happen quite so often. I've built my own handful of engines, and never had a problem with cavitation in the pump causing issues.
Often, there's a high spot spigot in the cooling system that you can open to "burp" air from the system. Do that, then close it when coolant starts coming out and finish filling the radiator afterward, and you're good to go.
Clacking noise, if light, will go away as the bearings wear in and seat. The clicking noise in the top end is likely mis-adjusted rockers, which need to be adjusted to clearances while warm for most engines. I'm sure someone can correct me on that, though, and I don't know the specs off hand for that engine.
I can't really say much more about the noises without hearing them directly, though.
Edit: Turns out you've already solved the problem.
Good that the noises went away, though the upper end noise may come back after the engine cools.