Hi Jon, thanks for replying!
Does creating a custom module in Java mean recompiling the LabKey's source code? If yes, then that is a scenario I was trying to avoid, but I would do it as a last resort.
However, could you comment on the following alternate approaches:
1. Write an R script to modify the template, which gets invoked through Javascript.
2. Don't have a .doc template, but an HTML one and modify it and let the user print it.