Dont ride your bike till the problem is fixed, since the bike is in the run-in period any slightest jerk can affect your bikes engine. And dont take it to your mechanic, only go to tvs service centres (till warranty ends, after that never go there :P)
My advice is just take it to a good tvs service centre and if required shout at them. Ask them to ride the bike and see. If they cant fix it, ask them for a replacement as there's still warranty left on it. Usually they refuses, then report this directly to the tvs head of your zone and he must do the needfull.You can also approach the consumer court if no response and demand for compensation (dont hesitate doing it).
Its not an Air filter problem, airfilter life is around 10,000 kms, you can usually clean and reuse the airfilter w/o much problems if it doesnt have any holes.
Choked air filter/ air passage might not be the reason , coz it occurs only at higher rpms if it was air supply problem. Anyways it might be an airfilter problem, if you have a dead rat in it or u placed something on the airflow passage under your seat.
btw you have your choke turned off ? I once met a guy with an fz16 when i went for my bikes servicing who was riding with his choke on without knowing and his complaint was bike jerking when goin at higher speeds.
Did you do your 1st service ?If not do it asap