Misfire - fuelling issue 2008 F650GS 800

OK so I did replace the stator and voltage regulator, battery at 12.8v standing and about 14.5v charging
HOWEVER
Took bike out this morning and all great until about 10 miles again, misfire/coughing. Turned round and got back home OK.
So whats next - I'd really like to diagnose this properly before forking out on replacements parts - bike, apart from this is a keeper, really like it.
If I get a Unicar Scan plus Motoscan - c £80 will that be able to see any faults on either the coils or fuel pump and controller. I'm thinking if Coils, EML light will come on so do we think Fuel pump, Filter and controller are best replaced first and dont bother with Scanner etc?
My commute is 26 miles each way so really need to trust bike to get there and back.
Thanks
On a completely different track, I had similar symptoms on a 2012 800GS and it was down to a faulty side-stand switch. Might be completely wrong, but worth a thought.
 
Fuel pump & filter
 
BMW estimates that the fuel pumps on the early 800’s (650’s) should last around 45,000 to 50,000 miles. I was quite lucky in that mine went at 78,000 miles, but not so lucky as I was in the USA. The symptoms you describe, the bike behaves like it’s running out of fuel, are a sure sign that it’s the fuel pump. When replacing it make sure you get a pump from the later, post 2013, bikes. They are a much better pump and will last very much longer.
 
BMW estimates that the fuel pumps on the early 800’s (650’s) should last around 45,000 to 50,000 miles. I was quite lucky in that mine went at 78,000 miles, but not so lucky as I was in the USA. The symptoms you describe, the bike behaves like it’s running out of fuel, are a sure sign that it’s the fuel pump. When replacing it make sure you get a pump from the later, post 2013, bikes. They are a much better pump and will last very much longer.
OK thanks, mine has done 41,000m but is 17 years old this year. I have bought a new fuel pump/strainer and fuel filter from Motorworks.

I watched the video on youtube of the Canadian chap replacing his, think I should be able to manage it.

Fingers crossed
 
I have had similar over the years on my F800GS. I never found the "real" reason, but i suspected the position of the fuel cap on the side of the bike. When its on the side stand, in the rain, i suspected water pooling around the filler cap and possibly getting into the fuel tank. I put in some expensive water remover, and have switched almost exclusively to E5 rather than E10, and haven't had a repeat of the problem (fingers crossed).
 
I would be surprised if enough rain got passed the fuel cap seals to cause a problem, Bobbsy. After I had got the new pump in Colorado the bike (a 2008 F800GS) sat out overnight in a number of tropical storms in Central and South America and I never had another issue. Even given the rather low quality fuel available in a number of countries. Have you checked the filler cap seals because it sounds like they need looking at and replacing.
 
Thanks SuperTed - yes i did replace seals, and also could have been a bad batch of fuel etc...just never did pin it down.

Good advice above on fuel pump, I'm around that mileage so will put it on the list.
 
Ok we are all fixed and bike future proofed.
Replaced fuel pump, filter and controller - still misfired.
Removed coils (one cracked) and plugs - looked like originals - replaced all and now running like it should. Original charging problem was separate issue - £270 on parts plus faffing - not bad.
 
OK thanks, mine has done 41,000m but is 17 years old this year. I have bought a new fuel pump/strainer and fuel filter from Motorworks.

I watched the video on youtube of the Canadian chap replacing his, think I should be able to manage it.

Fingers crossed
Hi do you have a name or link to the video you mention please
 


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