With my install i didnt slot those holes at all. Some beat the tower....others don't. Some say the 90 and up have a pinch more room.....
I think i couldve gotten the booster in without tapping the tower....but....i was frustrated as hell at the time. It took a friend to look at the studs coming through by the pedal for me to get it in. Real PITA.
He came buy after my wife called him ( her cousin ) 'cause i was bout to burn errything to the ground !!! It was the hardest thing I've done to date on a mustang.
You make it through this step without throwing tools and going into convulsions....you can conquer anything.