Help on my 1964 4 speed swap

Its not clearing because that whole section needs to come out, and a four speed tunnel (hump) needs to be installed. Once you get a tunnel laid in there, trace the outside of it with a Sharpie and cut and remove all the sheetmetal about 1" inside your line,leaving enough metal to weld the new floor hump to.
Go to brewersperformance.com to see what you need. Then place a wanted ad here to get your hump or order one from Brewer's- they carry new and used metal ones as well as fiberglass reproductions.