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Hello Ike! I did this install a few months back.
For question 1, the instructions that came with my kit indicated that removing the plate was necessary for clearance. I'm not sure exactly what that plate was originally intended to do, but most references I found called it the shift bracket floor plate. I used my borescope to make sure the cables/clips did not contact the carpet or anything else under there during installation before buttoning back up.
For question 2, those brass clips are there to prevent the shifter cables from backing out of the shift bracket. I found them "funky" when initially removing them, but reinstallation was a breeze, iirc. I would recommend reinstalling them as without them in place, the only thing holding the shift cables in the bracket is the outward pressure of the plastic clip design and the plastic-on-plastic friction.
Hope this helps. Best of luck!
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