The clutch issue I’m afraid you’ll have to get used to – they all do it from cold – oil changes help, but only for a limited time. Most of us rev it then stick it in gear holding the front brake (though I’ve heard of several different ways to do this, but personally lack the patience)
The vibration issue is far more simple – Yamaha introduced it as an indicator that the engine is running – in the absence of a rev counter on these things, the more it vibrates, the higher the revs. Wait till you get it up to 60mph, you’ll think it’s about to explode. It never will explode of course, but your fillings may rattle loose before you realise it’s just another charm that the humble TW has – that and a seat that will numb your nuts in under an hour.
The clunk in the forks also is normal – if you don’t have it, take it back to the dealer and complain …….
(Welcome to the asylum)