Using an external database to store survey questions and responses while using Drupal to display, submit, and validate them

I'm building a 500 question, multi-part survey, within a Drupal site and am wondering what the best practices are for storing and retrieving large data sets from an external MySQL database.

Here's what I'm trying to do:
- store questions and responses in an external database
- use Drupal's Form API to handle form display, submission, and validation
- have a Drupal user "own" a survey so that they can update their responses over time. For example, a user should be able to fill out 10 questions and then come back later to fill out the rest. Next year, they should be able to fill out a new version of the survey.

Has anyone done something similar before using Drupal? If so, do you have any recommendations? Is there another approach that would make more sense?