Hmmmm...there are no leaks (fuel/air) anywhere.
After installing the new manifold how was the MT behaving, was it erratic, dies out after a slight pull of the throttle? or during high speed?
If dies out after a slight pull of the throttle chances are that its to rich. Durig high speed it must be the high end needle of the carb.
Ooops, you still have the original engine with the single needle carb?
Try closing this fully, and opening it 2 1/2 turns out and start it out.
beyond that am stumped without actually being there to see it.
Paul