Hiya and welcome to XT660 com, the best site around. These guys are excellent.

In answer to your question you need to just take your time and read through this site, clicking on all of the relevant threads. Start slowly and dont worry, the XT660 is one of the most bulletproof bikes on the market so you cannot really do any damage.

The basics are really to save weight (so an after market exhaust will help straight away) and let the engine breathe better, on the inlet side you should consider the excellent DNA filters plus a snorkel removal.

Have fun and enjoy your bike.

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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....