well firstly welcome to the world of biking as for warming i up, there isn't really a set time, each bike (size,make,model,age) all have their own min time for warming up. really you'll have to find out ya self, but a couple of mins should do it. my friend starts his and lets it run while he has his morning fag. i only let mine run while i put my helmet and gloves on and walk it through the gate,by the time i done all that it's ready to go (colder mornings mine needs a while longer) as for the "clunk/thud" do you mean it's backfiring? it won't sound like a car backfire if it is that, it could be you're bike is running to rich ( too much petrol, not enough air) remove a spark plug if it's fouled. and check ya air filter box (i'm assuming you've got a standard box,not a pod) for obstructions. if the air filter is clean, there is a air/fuel mix screw on ya carb, make a tiny adjustment ( like 1/8th ) and write it down on some paper and put it in ya owners manual or log book or something, just so you know how much to take it back to what it was originally at, if you ever need to if it's no that, it could be a worn exhaust valve. there's a guy on here called walneyfranky ( or something like that) he'd be best to talk to about that