Didn't you have some of these issues before? Have you completely gone through the rigging and controls to make sure everything is correct per the manufacturers specs?

Also as the engine stopped - is it possible you had a little bit of water in the fuel - as you haven't flown it for some time? If it was fuel starved - it could cause shuddering.

Also keep in mind an engine will act/run differently when running under load (in the air) than it will static (not moving on the ground).