Moving over from a CBR, the SD is A LOT different, so i'm not sure what is normal/what isnt. Please bear with me as these are very dumb questions

Is it suppose to vibrate more as the revs get higher?
Is it suppose to clunk a lot below 3k? (specially in anything other than 1st)

Yeah and yeah. Sounds fairly normal mate.

Running aftermarket rearsets on mine and you can quickly see why they have rubber topped footrests as standard.

first time on a twin? (not taking a jab at ya) i'd expect more vibes in general compared to an il4 but others w/ a longer bike history can probably say more bout it
could you describe the clunk in more detail? sounds like you're describing how the shifting action feels/sounds, but not sure what ur referring to

Keep the revs up - if possible over 4000 rpm.
Your chain and transmission will thank you, as will your gas station.

In all seriousness, the minimum 4000 rpm was something suggested for twins to me a long time ago and I feel it holds true that twins need some revs to comfortable and not suffer from rough running or chain slap. The KTMs with their extremely light cranks even moreso.

You went from a sewing machine to a washing machine...learn your new bike and adjust to its likes/dislikes. 4000 on the low side and 8500 on the high will keep you in a real sweet range for twisty riding...learn to use the torque.

In regards to your question about general feel of the SD.

IT FEELS GOOD!!

Different bike, different caracter. You won't fall asleep and you enjoy every moment riding it.

I sometimes ride it with Harley drivers to have a coffee and sigar Cheapest as well, which is nonsense... The bike is just f..king fun to just cruise around, if you do not forget to play with the throttle and let it bark. Otherwise its worthless, you have to enjoy its character. Its a terrorist bike in nature.

You got dirt bike experience? That what this is ! A big dirt bike with lights and street tyres. Keep you left hand over the clutch and feather it to keep the rev's up. The clutch does not have to be ingagged all the time. The clutch has friction plates, kind of like brake pads. Slip the clutch! Get the rev's up, gas it into the power zone, then let the clutch out. The clutch is your friend. Good to feather the clutch on corners too if you see crap on the road to avoid high sides.
Take your bike for some long rides away from traffic and bond with it. You will figure it out. It's not really a city bike. Let it sniff out some twisty open roads with some elevation changes..
Wa Ho! ..... AND GAS IT !!.

Hi mate I too am a newbie to my duke coming from motercross to a few blades must say i am loving it but still some.in certaintey to it . feathering the clutch helps at start stops etc

I gave the farther in law a shot and he changed into second at maybe 15 mph and it made some horrible noises like what your talking about. I thought he was gonna kill.my baby lol

I find that 26 mph I can get away with 2 and gear trundling through the town but that's about as low as she will go with out being in first gear.

I'm gonna change my springs as I'm 16st so it strains the standard springs on my 08 SD not getting the most out the corners or my tyres lol still.got the bobbles on lol.