Ian, I just saw your post. The software upgrade is pretty short, should only take a few seconds, then a reboot. If it says ver. 5.3 down at the bottom of the screen on the reboot, you're all set.
You need to refer to the current install manual, rev. AB, I believe, for all your RS-232 port configurations. There will be specific protocols for each port outlined in the manual. I recommend that you make up a chart with all your ports, their functions, and the configuration protocol for that port. You should have an RS-232 icon on the main configuration page. Go there and start setting up your ports one at a time. It may take a little time to find the page for each port, but it is in the manual. If you PM me with your email address, I'll send you a PDF version of my RS-232 spreadsheet to serve as a guide.