Yeah the bike is used. I'm his best friend and we went to pick the bike up and originally the guy said the bike needed nothing , yeah right. We have put on a new throttle housing, bars, return throttle cable, new plug wires, new shift shaft seal, fixed a short, new horn, misc. lost bolts replaced, new tip over switch as the old was missing the rubber grommets, taken the exhaust off and cleaned and reinstalled it due to a leaky joint,new iridium plugs, also a friend of ours remapped it to better suit the Jardine RT1 that came on it. It has been running ok till the other day he called me up and said that the bike was knocking. We so I went over to his place and it wasn't knocking but it was Idleing weird as if on one cylinder so I told him to bring it to my house the next day. Well the next day when he came to my place it was running fine and I put mechanics stethascope all over the engine and it sounded fine. this engine isn't going to blow anytime soon due to structural integrity. No noise from the bottom, top, or primary.
Only things I can think are bad mapping(fouled plug), O2 sensor, wire harness. Any thoughts?