Seems all has been covered in the referring links, I would add one to it & that is your rear sprocket holder dampening rubbers, grab the rear sprocket & see if you can move it back & forwards, there should be no free play in the rubbers, if it has free play it will make the bike have a delay or jolt when coming off & on the throttle.

If there is free play renew the rubbers or carry out our rear sprocket rubber mod.

8/ Free play in sprocket holder mod.
http://www.xt660.com/showpost.php?p=113529&postcount=1
http://www.wemoto.com/bikes/Yamaha/X..._Rubber_-_Set/

The 04's were the hardest 660's to get smooth with the 00 ECU's, I would also do this mod for better throttle control.

13/ Twitchy Throttle, good mod to do.
http://www.xt660.com/showthread.php?p=154983#post154983

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Mods that I have done to my XTX's

My 04 XTX
Stage 1 & 2 DNA filters / Kev fuel mod / snorkel mod / Drilled air box mod / Engine breather mod / Fork Spacer mod / 15w fork oil /
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My 07 XTX
Raptor 700 cylinder 102mm / Modified Crank Case to take a 105mm Raptor Cylinder / 11:1 102mm JE Raptor piston / Stage 1 Raptor Hot Cam / Ported head / Colder Spark Plug / +2mm Throttle body / DNA stage 1 & 2 filters / Modified Air Box / Snorkel removed / Worry Brothers stage 2 filter cover / 6mm & 8mm Bolts Replaced with Titanium Bolts / Recovered seat in Black / O2 Eliminator /

My 09 XTX
59HP at the rear wheel / Stage 2 Raptor Hot Cam / DNA stage 3 Air Box / Carbon Can Exhausts / Modified Exhaust Link Pipes / PCIII With Custom Fuel Map / Wideband Commander O2 Data logger / LCD100 Dyno Jet display & fuel adjuster / 2500 OHM HT lead instead of a 10K OHM XT lead / Extra Coolant Cooler / Protaper Fat Bars / Tail Tidy With LED Tail Light / OKE Protection Knobs / LED indicators / AIS blocked / Modified rear sprocket rubbers / Rear Foot Pegs removed / 09 ECU With 02 Sensor Changed To A 06 ECU / Complete wiring harnes Changed from 09 to 04 / Home made LED resistor flasher / Hole drilled in the fuel tank filler neck to allow quicker filling / Modified Bar End Weights / Progressive front fork springs, 15W fork oil, forks lowered 25mm, used XTR rear links lowering the rear 20mm, rear spring one click stiffer / Changed front & rear guards from blue to black / 47T rear sprocket / Speedo Healer V4.0 / Kev throttle cam mod / Throttle grip mod / The new 2010 O2 sensor mod is out, works a treat, The new 2012 O2 Controller is out, PM me for details

Now ride a 2018 MT09SP ABS + TCS

My KTM 990 SMR Mod book. http://www.ktmsmt.com/viewtopic.php?f=13&t=4946