I am assuming some things here as your story is kind of incomplete. I am assuming you removed the air intake leading to the throttle body (that is where the throttle valve is). If indeed the engine runs better when you cover the throttle body that would indicate a substantial engine vacuum leak. You will need to do a complete inspection to try and find the cause of your vacuum leak. Possible causes would be the intake manifold itself, the intake gasket, any vacuum hoses or lines, the power brake booster, ect.. Is the check engine light on, if so are there any fault codes current?