Mine's just a single bracket above the centre console with long bolts and two spacers to prevent crushing of the plastic console. Some random thoughts...
How much are the holes out of alignment ?
I presume you've got the dash in place and that's what is causing the misalignment. Is it a new centre console ? As long as there's enough space to let the cables go smoothly through the big hole in the chassis I'm not sure it's a mission-critical thing, more of a "if it looks right, it is right".
My immediate reaction was that if the holes don't line up, drill new ones
Brian