What I want to do is modify a Perl CGI script so that the output (a load of html) is written to a file called output.htm rather than to the web browser. The reason for this is that the perl script takes a long time to run (it is doing many queries to a database), and so I want to make it a scheduled cron job.

I beg your pardon, but looking at the code you made available and the description above, seems to be that you don't need anyway to use a CGI. If you're going to query your database and execute the script in a regular basis using CRON, don't use CGI.

BUT considering that your CGI is receiving some parameters and using them in the query, then what you need is to detach the query from the CGI itself. My suggestion is, if you want to use cron anyway, just use write the information from the webuser somewhere in a way that the script, that you be executed later, read this information and generate the new HTML content.