and :welcome to
What is the year of manufacture of your bike?
The run of faulty ECU's went from 2004 to late 2006 until all subsequent production was fitted with an upgraded ECU. There is something else you need to check, in 2006 Yamaha issued a recall on a limited batch of XTX/XTR declaring a faulty TPS (throttle position sensor) which was not returning to a decent tickover on shut throttle. After that recall, everything was ok for most of those like me who had 2004 to 2007 bike.
But unfortunately Yamaha couldn't leave things as they were, in 2007 they added a Lambda probe (O2 sensor) connected to the ECU which made thing worst by stopping a Power Commander or any fuel mod to work, and that was when Kev, our in house mechanic guru, started to work on his new mod that included an O2 eliminator.
So we recommend you get one and solve all your problems.
To be precise if your bike is a 2004 - 2006 production all you need is The Kev Mod without O2 eliminator see this link
https://www.xt660.com/home/kev-shop/#fuel-mod
If your bike is a 2007 onward production then you'll need also the O2 eliminator and that is included with the mod follow this link:
https://www.xt660.com/home/kev-shop/...r-and-fuel-mod
If you want to go the Power Commader way and have your bike Dyno'ed by a qualified DynoJet Centre you will need to purchase a DynoJet O2 sensor eliminator otherwise the engineer will not be able to work out a map and the PCommader won't work without on a 2007 production model.
Hope that helps, but please if your bike is a 2006-2007 model give your chassis number to an official Yamaha dealer and ask them if your bike was within the TPS recall or not, and if it was you can demand a replacement because the recall was official in the papers.
Good luck