I would suspect the motor mounts for your shifter alignment problem, but not matter how bad they are, they wouldnt cause the pressure plate to rub the bellhousing.
Are you sure that its hitting it and not just the throwout bearing gone bad?
If it goes away when stepping on the clutch, this wouldn't be the pressure plate then, since it does not move when the clutch pedal is pressed. Are you sure you put the clutch in the correct way with "engine side" facing the engine?
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NMRA O/C 9516
NA pumpgas stickshift 347 10.65@125.6, 6.73@100, 1.41 60ft
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