How do you fix this?

Where is your shifter as it comes through the floor? Is it close to the gas pedal or closer to the seat. If it's back toward the seat I'll bet you have a B or E body transmission. The B & E trans' have a longer tail shaft and the drive shaft would have to be shortened to make it fit. (Your vibration problem?)
The shifter mounting bosses near the tail end of the trans in picture #1 is the B and E body mount. The rods would have to go through the cross-member to get to the shift levers I'll bet. The blurry photo on the bottom is the tranny out of my 66. The tail shaft is short and she 1-2 and 3-4 shift levers go between the cross-member and the case. The reverse lever loops down below the cross-member.

mopp_0606_05z+dodge_transmission+four_speed_housing.jpg

032800951542[00].jpg