Where did you drill the exhaust? The cat is at the very bottom of the exhaust near the link pipe.

If the exhaust is now allowing more flow you will need to increase the CO & up the idle speed to stop it cutting out.

Can you do a favor for me can you remove your left side black cover & give me the numbers off your Engine ECU, I want to see if the 2010 models are running a different ECU.

This is what you are looking for.
http://www.xt660.com/showthread.php?t=8546

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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