There are two holes where the rods attach to the linkage going into the Trans. The factory always used the top holes. If you move the linkage to the bottom holes the shift will be much closer and will not hit the console.
If you have an AIM you will see the two sets of holes and know what you are looking for before getting under your vette.
The other thing that happens is a lot of times when the console is removed it is not reinstalled forward enough.
It is not easy to get the console in the right position and you will need a lot of patience but the console and lower dash panels will fit better and you should no longer hit the front of the shifter opening plate.
All this should be done after you make sure all of the bushings are still there and the linkage is not bent.
If you do all these things, assuming it is the original shifter, the car will shift tighter than it did new!
Bill