2003 Bonni won't stay running

:banghead:Our 2003 Pontiac Bonnivllle just had the transmission replaced at 160,000 miles. It still shifts hard and NOW car has very hard time starting with strong carbon smell and will idle rough. Motor mounts were removed for transmission and have checked harness on drivers side fender. Beat heck out of catalytic converter and will run after that sometimes. Any ideas?

Dumb question, did you start the car with the exhaust pipe disconnected from the rear manifold to see if you had a partial or plugged up CAT?