(Excuse my English, it�s not my native language. I�m Greek, living in Crete.)

History:
XT 660 R, 2004 model, problematic TPS was changed by Yamaha for free, good condition, 30,000 kms (19,000 miles), prior owner is a gentle and careful rider. I bought it 10 days ago. I visited Yamaha authorized service, where they detected a very slow idle speed (around 1,000RPM) which they raised to normal.

The issue:
If we divide throttle opening in a scale from 0% to 100%, the bike runs fine from 20% and above. Real power, excellent acceleration.
The problem appears under this 20%, when i.e. I want to keep a steady speed of 70 or 80 kms/h, (47mph) which is my usual way of driving. Engine goes up and down, as if the injector doesn�t know how much to spray. The feeling is that engine does on-off continually.
Things get worse when I close the throttle a little bit more (not entirely), let�s say to the 5% of this theoretical scale. The ups and downs become severe. The bike trembles. Turning the throttle off (0%), this �sawing� stops, but the bike decelerates more than I wished it to.

Some solutions I�ve read around the web:
Use better fuel (100 octane�s)
Enrich the gas-air mixture
Change air filter (mine is brand-new)
Decrease the input of air temperature sensor on purpose, so ECU senses �cold�

I don�t agree with any of the above and I can�t accept that this bike was constructed to behave like that. Any ideas -or links to similar previous posts- would be very helpful to me.

Although it wasn't designed to be like that, sadly a lot of them are!

Have a read through the threads in the links below. They will give you some ideas as to mods that can be done to smooth out your XT...

(1) Join XT660.com supporters to access the “Ask Kev” 1:1 technical help section - http://www.xt660.com/payments.php

(2) Check you haven’t got a dodgy TPS (which you’ve already done and got fixed) - http://www.xt660.com/showthread.php?t=948 Yamaha Recall

(3) Check you haven’t got a dodgy ECU - http://www.xt660.com/showthread.php?t=519 Yamaha Recall http://www.xt660.com/showthread.php?t=8546 (How to recognise the different ECUs)

(4) Twist-grip mod - http://www.xt660.com/showthread.php?p=154983

(5) Cush drive rubber mod - http://www.xt660.com/showthread.php?t=12422

(6) Adjust your CO - http://www.xt660.com/showthread.php?t=55

(7) Adjust your TPS - http://www.xt660.com/showthread.php?t=56

(8) Fit Kev’s fuel mod - http://www.xt660.com/showthread.php?t=194

Click on the link in my signature for the full list of all the mods available – and it’s a long one!

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Thanks a lot, I will read all of the above links

Another one to check is the chain tension, on the xt range a slightly too slack or loose chain can make it feel like what you describe.

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Plough on

Thank you for the advise to check the chain tension, my engineer did that today, but ups and downs go on... I'm thinking of changing the ECU 5VK-8591-A00 with ECU 5VK-8591-A01 from 2005-2006 models. Has anybody tried that?
Thanks again

The 01 ECU was used as a replacement by Yamaha to cure surging on early 00 ECU equipped bikes, so it's been tried and tested.

Changing to an 01 ECU will make a big improvement in reducing surging, in fact it can almost be completely cured on an 01 ECU with a fuel mod or Power Commander.

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