Try the engine on a test stand. With many 3D-type airplanes, the airframe is not particularly robust. This allows engine vibrations to get to the fuel tank and agitate air into the fuel. This can easily cause running problems. If you can't get enough foam rubber around the tank to isolate it from the engine, you'll have to go to a smaller tank that will give you the room you need, or go to a vibration-isolating engine mount.

A test stand will tell you if the engine's the problem or the airframe/engine/mount/fuel system combination is the problem.