1996 Nissan Pathfinder Studdering bad gas mileage hesitation

It all started when we had a timing belt tensioner broke and we had that replaced and while that was being done the mechanic also changed the water pump and put a 2003 transmission in the pathfinder. Since then it has been studdering while it's being drove and it hesitates really bad on take off and when your going up hill or if your trying to pass someone then it will shoot off like a rocket. We have put a new distributor on it andcap and rotor, new mass air flow sensor, new knock sensor, changed the fuel filter. What else should we check? The mechanic is as puzzled by it as we are. It has the multiple misfire code on the check engine light. When we have disconnected the battery to put the distributor on the light went off and the hesitation is a lot worse when the light is off and the studdering is some worse also. Do you all have any suggestions on where to go from here?
Thank you