"Im wondering what options I have for the user selecting the option, closing the document and then the script carrying on with the rest." Rest of what?
If the code has to be in Access, then we're talking Automation when it comes to controlling Office programs from other Office programs. If you want Access to control Word, then I don't get how you expect to affect a document if it's closed (beyond some of its inherent file properties) - or are you not saying that?
Or are you expecting Access to control Word to some degree, then allow user to work with the Word document, then pass control back to Access? All the user has to do is minimize Word and click your waiting message or modal form and Access code will resume and the document gets modified by the user. That is asking for trouble. If you're going to automate as you mention in the beginning, then why allow the user to act on a Word document?
The more we hear silence, the more we begin to think about our value in this universe.
Paraphrase of Professor Brian Cox.