Picked up my xt660r a month ago and it's totally stock. Fuelling felt ok if a little hesitant at low revs and a bit of surging at constant throttle.

A friend has a CO meter so we removed the snorkel and looked at the fuelling. CO was 0.6% standard with snorkel removed which is way too lean. A look at the CO in diag mode and it was set at 6 so we increased it 10 points and this increased the CO by 1% so we oncreased it another 10 points and left CO at 2.6% which is a lot better and maybe a touch high for the cats....
Bike rode better but there is still some surging especially when trying to control the throttle for balancing on one wheel, it felt like it wanted more fuel but didn't really want to increase it with the cats still in exhausts. So next step was to re-fit the snorkel and trim the CO back by 10 points. It is now all stock and the only mod is increasing fuel 10 points.

This is much better, holds a constant throttle even at very low speeds and is happy to fuel with tiny throttle openings on one wheel.

I guess if you have tried all sorts it may be worth returning to stock and just trying a bit more fuel from the diag mode

Thanks for your input, yes they do run to lean & require extra fuel to run better, glad your bike is running better for you.

This subject has been covered in the modification index, have a look sometime heaps of info there.

http://www.xt660.com/showthread.php?t=630

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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