Scripts cannot modify or create layouts.
You could create a new updated copy of your file and create a script in the file that systematically imports all data from the current copy of the file and updates any serial number setttings. You can then send out a clone (file with no records present) of this file to all users with instructions to click a button to import all their data from the old file into the new.
Shucks! Unfortunately, I inherited this database and it is a mess. There are 64 tables and 101 relationships...just to start with. I still haven't worked through the whole design report and determined what all is happening within the database. (There are some poorly written scripts, broken links, etc.) It looks like trying to import the data correctly is going to be quite an undertaking. The modified layouts affect just a minor portion of the whole database, yet necessary for an annual data updating process.
Your other option is to split your database into two files. File 1 contains all your layouts, scripts, value lists and such. File 2 contains all the tables--and can for the moment simply be your current copy of the file. In file 1, you start with a copy of the original file and then take each table occurrence in your relationship graph and point it at a table in the original file. Then you can update the layouts and distribute this copy to your customers with instructions to place it next to the original file. The main draw back here is that there is nothing to stop your users from accidentally opening and using the original file that is now serving as your "back end".