f650 gs Dakar miss fire...
I had similar problem last year,
New spark plug fitted you say, well have you tried an Irdium plug as this sorts out a slight stutter around the 3-4tho revs. Also remove the metal sheath around the plug cap (HT lead

I think this is)
I had a miss fire whilst travelling across Europe Sept/Oct 2007. I got off the ferry at Dunkirk and the Dakar would miss fire once and then again maybe 5miles on. I knew I needed fuel as I only put in the minimum at Dover...£5.00. I filled up in Belgium somewhere and set off only 20 miles further it would just falter miss a beat and sometimes when slowing down to go through a toll station it would almost splutter and feel like the rear tyre might lock up.
Anyway, I was thinking that whilst on the ferry i`ve strapped the bike down, turned the handle-bars really tight against the headstock and maybe crimped a wire. I had to take the Dakar into a dealer/service in Berlin and let them test it on the plug in machine. They said it shows 2 problems and can get the parts and fit them the day after. New fuel filter and new fuel pump. Well, I wasn`t going to argue but I just didn`t feel that this was the problem. OK! I said get it done and i`ll be on my way. Lots of Euros later I headed on to Poland. Well, I still had the same problem some 40miles into my journey. I returned later in the week for them to find the problem and that they won`t be getting anymore money. They did find something but it took them 4 days to find that a wire had crimped or fraided and they did not charge me anymore.
To be honest I still don`t know what they did as electrics just goes way over my head in understanding...
Just my pennies worth...and if you understand electrics...then it might just be what I had somewhere around and under the headstock as that is where cables move backwards and forwards.
Hope this helps...Dakarnoway