So just to verify you checked the bolt on the pulley or did you just check it with your hands?
did you try to wiggle the exhaust? I know mine makes a kncking sound by the rear end.
Also, turn it on and push in the clutch. See if the noise goes away. If it does you know its AFTER the tranny. If its automatic, you can unbolt the TC from the flywheel to see if its still the motor.
Next step is a compression check! <eek!>