The Running Man.

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I'm assuming these three lights come on and go off at the same time. One quick test I would try would be to remove the blue wire from the alternator. If that also stops the other two lights from flashing on and off again, the alternator might be the problem area.

It would probably be good to check the voltage across the battery before this test.

I ouched at that price so I decided to take apart ignition switch my self and rebuild.  Did not find that much corrosion inside the contacts but when I put together again and installed, problem went away.  Now I got to work on the warning lights.  the low fuel light, the overheating light, and the discharging light come on sporadically and then go off. 

. . . you need to be deliberate with the shift lever as it is possible to miss a gear. . .

Affirmative! If you are firm when you shift and are still getting neutral or having difficulty changing gear there could be two common conditions involved.

1. Improper clutch adjustment. Do a basic clutch adjustment right now. Use the instructions in BMW's workshop manual downloadable from the Technical Directory here.

2. Dry transmission input/clutch hub splines cause difficulty shifting if the clutch adjustment is correct. They get lubed with a paste ≈50% molybdenum every 40K miles.

Clutch discs do wear out and can cause difficult shifting also. If you perform a basic adjustment by the book and still have difficulty shifting using a clutch cable that's in good condition, you'll need to inspect the clutch assembly, at which time the transmission input spines can be lubricated.

Hello, I believe to have fixed my issue.

Got the new fuel filters through in the post, puffing a small amount of air through them in the correct direction revealed that the old filter was very much blocked up. After replacing filter and fuel lines in the tank, the bike rides fine, however still smells pretty bad when you give it some throttle. I'm still having my fingers crossed for now, as the issue only came up suddenly after I'd ridden through three quarters of a tank, so want to run through at least a couple more tanks of fuel to empty before I deem it 'fixed' fixed. I filled it to the brim with premium and will chuck some liqui moly injector cleaner in there too for good measure. I'm going to check the plugs and mpg after a few hundred miles and see if it's running out of spec. Another curious observation is that the temp gauge in the fairing is now hanging out at 1/4 of the way up (a bit above the blue) whereas before changing the filter it was bang on halfway. Exact same motorway ride on similar temperature days, riding the same speed in the same gear...

Next up is to change final drive and gearbox oil as I don't know when it was last done. Is it normal to have a neutral between every gear if you're gentle with the shifter?

Cheers for all your help lads
Tom