Okay, a couple of things going on here.
First, do you actually have a four speed floor hump for the car? If so, did you get the '65 and earlier floor hump, or the '66 only floor hump? Either one will work, with a few caveats.
The '66 has an oval shifter hole, the '65 and earlier one has a round hole. Not a biggie, right? The problem is that the '65 and earlier used a different shifter angle than '66 and later, use of the later shifter and mounting plate will cause interference issues when used in the earlier round-hole hump. The early shifter can be used in the later oval hole hump, however.
Early hump:
View attachment 1716123510
'66 hump:
View attachment 1716123511
When you say you have a '65 transmission, are you sure? The '65 and earlier trans has a ball and trunnion output shaft, the '66 and later has a slip yoke output. '65 and earlier shifter mechanisms mount at a different angle than '66 and later, in order to locate properly in the floor hump shifter hole. I can't tell from your pictures if the mounting plate is the early or late version, it should be #2298, IIRC.
All this means is that either floor hump will fit, if the complimentary mechanisms are also used. The one possible issue with using a '66 floor hump in a '65 or earlier car is that you may have some interference issues with your bucket seats since the hump is physically bigger- in '66 they made the seats slightly smaller to compensate.
To make a long story short (oops, too late), have your floor hump on hand before you remove too much metal. Lay it in place and make sure the shifter locates correctly in the shifter hole. Then trim out the sheet metal under the hump as I outlined earlier. And no, you don't cut the crossmember. Just the sheet metal! Then weld it in.
