I guess that eliminate the transmission as a cause.
When you say "shaking", is it just vibration a in rough idle? Maybe someone needs to check if the engine as a whole is shaking or is it something internal that's being transferred to the body.
I still think it is motor mounts. Try this. Hood open, engine running, transmission in gear, foot in brake, give it gas. Ask someone to see if the engine moves when gas is given. Can't think of anything else.