That click/clack may be the auto de-compressor sticking briefly. It sometimes manifests as a loud clack when the the bike wont fire up immediately.
Are you sure the stuff on the screen was metal? The magnets usually catch the metal. The screen tends to get covered in bits of grey gasket sealant at the first oil change - it's a bit startling because it looks like shards of metal!
The idle does speed up after you've put some miles on the bike. There is a large flat horizontal brass screw above the throttle assembly to adjust it - a bit tricky to get to without a bent screwdriver. DON'T touch anything else down there!
You'll notice a very satisfying increase in smoothness and performance over the first 1000 miles, particularly at around 500.
My bike too has always had quite a bit of mechanical engine noise. I assumed it was normal - old style single and all that. But I have heard a couple of other UCE bikes running, and they were virtually silent by comparison. I am a big fan of these bikes, but I do suspect there is a good deal of variation in assembly skills / standards of workmanship at the RE factory, and an unacceptably "relaxed" approach to quality control.
I don't think having a noisy engine is necessarily cause for concern - just the luck of the Chennai draw. Things will improve I daresay as more and more of these bikes are bought where Japaneses standards of build & finish have become the norm. Complacency is what did for the British bike industry after all - of which Chennai is the last outpost - but hopefully not the last gasp.......
I hope all is well with your bike Jake, it probably is. Enjoy the good bits. That 2 year warranty does remove a lot of the anxiety.....