well i couldn't take it any longer so I just went out and took a look under my car. The metal/metal contact noise I hear/feel is definitely the bottom of the shifter hitting on the exhaust heat shield. This somehow happened as a result of over revving. The D bushing is almost fully out of place, i have ES bushings sitting on my dresser ready to go. So I need to figure out why the shifter is now lower than before, and put the new bushings in, change trans fluid and see how the car feels from there.