I dealt with a similar issue. It was legal documents in WA state with line numbers every 3rd line and horizontal and vertical bars at specific measurements and specific widths. I ran into problems when trying to save those as HTML files. The format for the legal documents was very important, and I had a really hard time making the HTML output correctly. Frankly, I never got it to work right.

So, I ended up using perl to write text files that contained data the user had typed into fields in a web form. When they hit submit IN INTERNET EXPLORER, perl would write a file and then spit out code to make the browser execute the MS Word document and I scripted the mail merge with the data in the file. It was a hackish solution that wouldn't work on a public web page, but it was fine for this two person office.

The other thing I explored was Adobe Acrobat. They have a scripted way to insert data into fields, and a perl interface already written. If they are willing to splurge on the cost of Acrobat and translate all their documents to PDFs, you could use PDF Forms (FDF?) and easily script them in perl.