I adjusted the timing a little more (while I was just screwing around with it) and I got it to cycle mainly between -40 and -30 rad/s without any issues.
Turn up the frequency un the settings. It happens because they like go into eachother and vibrate. The frequency make them go inside of eachother less.
On the springs that connect the cylinders to the flywheel, try making the damping extremely high, with an extremely high constant. This will prevent it from spazzing out ang give you a stiff connection.