This thread provides you with a walkthrough for checking/deleting stored codes (post #2 onwards): -
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https://www.yamahasupertenere.com/index.php?threads/2014-super-tenere-fault-code-deletion-how-to.17354/#post-374664
This should always be the first step, when researching a potential issue with the bike - hopefully it may add direction.
I have to say I was never convinced by your special starting procedure - the start & stumble habit always seemed to point towards a problem emerging.
Maybe you have managed to find a work around rather than a solution. You have mods that will serve to lean out the stock fuelling which should be adjusted, within certain parameters, by the lambda sensors parts #4 & 5 in this diagram: -
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https://www.fowlersparts.co.uk/parts/5944967/xt1200z-super-tenere/exhaust
However, it is all too easy for one of these O2/Lambda sensors to become contaminated or start to fail, sending inaccurate readings to the bike's ECU. I'll let this piece from Denso explain: -
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https://www.denso-am.eu/products/automotive-aftermarket/engine-management-systems/lambda-sensors/how-they-work/
So, to conclude, whilst the dash is not shouting at you, let's have a check for codes first.