That whole arrangement is a royal PITA! The flimsy bracket will bend easily, and if it's not in exactly the right shape, the control won't fit right. First, make sure that you are using the right screws: they should be two beveled (counter sunk) sheet metal screws. If they've got a rounded head, they won't work.
Try taking the bracket (with the control mounted with the two screws) and bending the lower right and left corners downward, such that it will sit higher in the console when you place it back in. If the shift plate doesn't sit tight on the control before you screw the shift plate down, bend them down a bit more.
If it helps, I had to do mine about ten times to get it right...
Darryl
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"Let them that don't want none have memories of not gettin' any."
- Brother Dave Gardner