I did the auto to 4 spd swap. I did not remove the rear console bracket, had hopes of attaching some sort of center storage/cup holder like on newer cars/trucks. The 4 speed carpet fits over the bracket no problem. When installing the carpet I ran two bolts w/ captive washers thru the carpet into the console bracket just to keep the carpet located during installation. The two bolts are still sitting there, I just haven't found a center console I like. If you find one you like let us know what you chose. New ideas are always good.
If you need other general info on the swap, in the archives I submitted a post for auto to 4 speed swap.