Sounds like your mechanic is taking you for a ride to me ... I've never heard of replacing an intake manifold ... unless he was just talking intake manifold gasket ...
How did the car run before you took it to him? definitly get a second opinion ... and if you feel comfortable with the second opinion show him the list of things that were supposably changed by the other guy & ask if they were done, & if the other guy could have caused these problems. Sounds to me that your car was running fine, you wanted the exhaust changed & then he told you that you needed alot of work, then you get the car back & it runs bad ... so now you keep coming back & getting things fixed (changed) until you get tired of making a car payment to him every month & go buy something new ... just my