It has happened 2-3 times the last year and they had in common it was raining. The engine stalls and eventually dies as I drive. If left 5-10 mins it starts normally again. So I suspect it is a water intrusion issue but I wonder where?
At the same time the headlight switch has weirdly started functioning in the inverse sense. Flip the switch for short beam and you get the long one and the other way round. Any ideas?

It is XT660R. I look at the bulb but the lighting effect on the road is commensurate. The small bulb is always on by design. The big straight bulb toggles on and off with the switch but in the inverse sense.

I think you've actually got two problems going on here. It's just coincidence that they've cropped up at the same time, although water could be a common denominator.

As for the stalling in wet weather, 99 times out of 100 this is down to water ingress in the joint between HT lead and coil on XTs - It is a very common issue. The standard fix is to dry everything out, make sure the plug cap is in good condition and connected to the HT lead securely and also that the HT lead is connected properly to the coil. You need then to coat all the joints with silicone grease to stop any moisture getting back in there.

The headlight is a bit more of a mystery! Water could have got in the switch and caused corrosion or bridged connections, but the way the switch is wired I wouldn't expect the symptoms to be reversed switch operation. There are numerous possible causes all of which are difficult to pin point without actually having the bike to look at, but hears some things to get you going:

Take the switch apart and check everything is as it should be inside, clean, dry and free from corrosion. Maybe give it a clean out with contact cleaner (or brake cleaner) - do not use WD-40!

Follow the wiring from switch to loom connector and to the headlight bulb connector. Make sure there are no abrasions in the insulation and that the connectors are clean and water/corrosion free. Also check that there are no reversed connections while you're at it. Dry everything out if wet. Clean and apply dielectric grease inside connectors and silicone grease round the outside when they are snapped home.

Try a different headlamp bulb. There may be an internal fault in the bulb between filaments and it's external connectors. Vibration on singles gives bulbs a hard time and it isn't unheard of for cheap H4 bulbs to have been made/wired up incorrectly!

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Hi, I partly removed the fuel tank today, exposed the igniter coil, and started the engine. I then spayed water all over. I couldn't replicate the problem. When a couple of times the engine stalled I was spraying on the air cut-off valve not the igniter. But this does not explain the problem, does it? This valve opens and closes and directs intake air to the exhaust.

I had a similar problem with cutting out after leaving my XT parked in the rain for a couple of days, turned out to be that water had got into the killswitch. I took it apart fully and cleaned the contacts with WD-40 and has been fine ever since!

Re stalling in heavy rain.....I'm no electrical expert but my brother had exactly the same problem with a triumph scrambler....it was the rectifier...which was exposed on that bike much as it is on the xt range....