I've completed my bare-bones version of the web-based record search tool. All of the logic for the search - both displaying the available options and parsing out a form submission - is contained within two classes, Search and Search_Form. The classes build the search query in an organized manner based on passed parameters. This format makes the search easy to change or extend, which I can foresee happening based on the needs of the data and the researcher SD. All of the code is documented using comments and standard docblock syntax.
The database-side of things is handled with Zend_Db, the Zend Framework's RDBMS adapter. Since the search form can result in some very complex queries, Zend_Db makes the process of building the select statement relatively easy. Plus, it's a more robust database adapter in terms of security and integrity than I could build in any decent amount of time.
The search form doesn't yet have any styling and is bare, but now that the functionality is done everything else will fall into place eventually. SD is coming in for a meeting Thursday Jan 27th so I hope to hammer out some more details then.