Just thought I'd post a little update seeing as we seem to have resolved the issues now.

My mechanic friend believes that the KTM workshop opened up the head, replaced the 2 intake valves, realised they didn't know what they were doing, stuck everything back together (without replacing the head gasket), wrongly set the timing chain and the valve adjustment. Also the throttle position sensor was a mile out set in the complete opposite setting.

Long story short, we had to replace the head gasket as there was signs of radiator water getting into the head. Whilst it was opened, we overhauled the water pump but all the rockers and cam follower bearings etc were fine, no play at all :)

So the list of work done would be something like the following:
Chain/sprocket replacement
New air filter (old one was actually disintegrating)
Fork seals
Throttle position sensor adjust
Top end overhaul and gasket
Compression test - all good
Intake valves replaced
Water pump overhaul
New radiator fan (bearings were seizing, not 'cool' in Malaysian temps..it's now wired to be on all the time with the ignition)
New battery
Wiring around the radiator was damaged which was causing the frequent fuses blowing - repaired
Accessory socket connections were the wrong way round...adjusted

So all in all, quite a bit of work was needed in the end (not helped by the KTM shop..)

Took it out for it's first proper run yesterday (after checking the headbolt tension last week after a few short local runs), did about 200kms and no issues :)

However the non-original (no name) exhaust is bloody loud and is still popping on deceleration. Won't change it straight away but think will look into alternatives, any suggestions for a replacement can?

It was doing 160km/h at 7,000 rpm. But still think it could do with a bit more 'oomph' in acceleration although it's way better now. Is replacing the can essential or can this be done by removing the snorkel and changing the jets?

ps thanks for the great info, all of which was useful :)

pps after a couple of out of town rides and some dirt roads, fuel economy was around 19-20km/L which is up on the previous 13.5km/L when it wasn't running well

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Nice work Mike! Beautiful bike! Worth the investment I'd think. bier

De-Cell popping is normal but really noticeable when running a loud pipe. Ditch that pipe! Changing jetting can alter popping but for the most part it will be there
no matter what.

Best look to 640 experts for suggestions on opening air box, changing needle and re-jetting. If done right, the BST40 carb has a lot of potential to get the most out of your bike ... and still get decent fuel economy. Lots of options. :thumbup1:

There must be other pipes you can run that breath well but aren't obnoxious.

Good luck, keep an eye on the head gasket, rockers and valve clearance.

Got a FCR 41 installed some weeks ago on my 2002 640 Adv, a much better bike!

Little update since I relocated to Penang a couple of months ago. I got a local mechanic recommended to me re-jet it without changing the exhaust and there was huge difference in the power delivery and also a reduction in the exhaust popping.

Just been for a 5 day jaunt to Thailand and it behaved very well on and off the highway. Still getting around 19km/L running the 16/42 sprockets. Couldn't tell you what jetting was used (I did ask..) but happy with results although I am curious on the FCR41 and different gearing options..I guess it's all a work in progress ;)