YOu can create a script or an action that takes your modified PDF form and applies all the scripts (document level, document event handler or field event handler scripts) wherever a script is necessary.
You need to figure out what's easier to do, update all field positions manually or write a script that modifies an updated document for you. this also depends on how many updates you anticipate. For forms that get updated often, I use such scripts, form forms where updates are infrequent, I just move the fields.