How do you fix this?

From what I can see from the photo you have an A body trans. The problem is the shift linkage is suppost too go over the top of the crossmember and between the frame and the floor, If it had the factory floor hump. I take it the linkage go through the crossmember and then is bent upward to the shift levers on the trans. Should go up at the shifter and then straight over to the shift levers. The trans mount does not look right ether, look one up on brewersperformance.com to see the right one. If it was mine I would get the floor hump, crossmember, and shift linkage and fix the frame and put in a new trans mount, this should fix your problems.