well it could be the problem of jetting, but i think its the problem of the ignition and low rpms, i say this because my friend has an am6 bike and we were mounting an mk prorace 2 cyl on with his standard igition. on low revs (half throttle) it sounds terrible, no power but once you give the full throttle the bike wheelies up to 4th gear...i was reading the manual booklet of the pr2 and it recommends a competition ignition...he is soon getting the pvl digital variable and his problem will be solved..
maybe this might be your problem, that if you have a standard ignition on it might not be good for your setup.