Remove the cable at the shift plate and pull it back through the housing. Tie a string on it so you can pull the cable back through once the boot is installed
Your saying just the outer jacket of the shift cable is larger then the hole in the boot? If this is correct, then your OK, it should fit tight. Put some soap or oil on it and it will slide on.
Now if you have not removed the entire cable from the boat yet, you need to do it first