Should I stop all programs during monitoring, including my firewall and my antivirus?

This is a very good question! :) The reason why you should stop other programs is the following.

If you monitor an installation and, along with the installation (setup) program, other programs are running, then both the setup's actions and the other running programs' actions will be recorded in the install log file.

Later when you uninstall the program using the installation log, all the actions recorded in the install log will be undone. If the install log contains just the actions that the setup program did, then only those actions will be reversed (undone). That means that the program will be removed (uninstalled) correctly.

If the install log contains, along with the setup program's actions, the actions performed by other programs, then both the actions performed by the setup program and the actions performed by the other programs that were running at the time you monitored the install will be undone. This is not a correct uninstall because it involves undoing actions done by the other programs, which have nothing to do with the setup!

The answer to your question is that, theoretically, you should stop all programs. Practically, because stopping both the firewall and the antivirus means taking some risks, you can let the firewall run in the system tray.

From our point of view, the only thing that a firewall could do is saving a log of stopped attacks during the monitoring process. This means that when uninstalling the program you monitored you would also delete the firewall's log file. Which is not such a bad thing! :)

As for the antivirus, the only bad thing that might happen is that if it will perform an automatic update during monitoring, this update might be deleted later because it would appear in the installation log of the monitored program. Also, if the antivirus would automatically start scanning during monitoring - your system could slow down a lot and even seem to be halted.

Final answer: you can leave the firewall in the system tray but I recommend you to stop the antivirus (or at least disable it's auto-update and live scanning features while monitoring).