Non expert here but it sounds to me that for problem 1 and 2 you must increase your idle speed slightly, and for problem 3 it sounds like your disc is slightly warped???

Good luck...

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(Now sold on, sob) 2011 Blue XT660X with gold wheels, was 26,500 km.
Engine mods: K&N Stage 1 filter, DNA Stage 2 filter, snorkel removed, Kev fuel mod fitted.
Plus: smoked Puig screen, Yam aluminium sump guard, Yamaha / Acerbis handguards, Givi Trekker aluminium side cases, Leo Vince X3 cans plus Kev front fork mod and Fender Xtender. Just fitted Michelin Road Pilot 3 tyres.

SOLD the XTX for a Super Ten 1200. And just bought a Raptor 700 so staying on here for some tips....