If I can venture an opinion, maybe you should check your air filter. Why would it suddenly start doing it at 2600 miles? These bikes are very sensitive to correct fuel mixture.
Mine also developed intermittent surging problems at low revs after cleaning the DNA filter (at about 4300km) and I had to play around with the CO mixture to get it right again.

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2014 XT660Z - Barrett pipe, DNA stage1.5, Barkbuster hand guards and handlebars, Pivot pegs, Teknik suspension, Guard-it engine protector combo, B&B rear rack, Trax topbox.