1989 Mazda b2200 smoke, studder, transmition

hi i have a 1989 mazda b2200 2.2L and when i start it, its starts just fine just smokes for like 5 minutes then stops and it takes off ok but sometime when i take off i studders like im missing a cylinder im putting a new valve cover gasket on monday because the old one is cracking, will this help maybe the compression was low because the gasket? and another when i down shift my truck makes a whining noise, do i need a front main seal for the transmition, oh and by the way i just replaced the front main seal on the front of the motor if that helps any.