Aye Gareth,
I dinnae like the sound of that description.
and strangely the RH exhaust can gets substantially hotter than the left.
To me that reads like you have a left-hand exhaust valve that isn't sealing properly!
Also check out the lambda sensor in the exhaust, so a software "plug in" to your laptop, or a visit to somebody who knows what they are doing with a dynamometer!
Am I correct in assuming that this is the Yamaha XT660/MT03 660cc engine?
Not sure who might assist in South Wales, but it might be worth a telephone call to Slipstream Tuning; if these boys don't know, they will have a good idea.
Slipstream Tuning contact details:
Slipstream_TuningGood health, Bill