Does unit2 look like it has a valid configuration? If it does, then yes, it would be good to upgrade unit2 while standby to 9.4.5, install HF2, fail over to it, check that traffic processes correctly and then upgrade unit1. You could install 9.4.5 on a second harddrive slot and leave 9.4.3 on the current active slot. This gives you two methods for backing out the upgrade in the event of a problem: failing over to the peer unit on the original version or using switchboot to boot back to the 9.4.3 slot on unit2.
You can get details on the switchboot command in SOL5658:
SOL5658: Overview of the switchboot utility (
Click here)
If the configuration on unit2 is suspect, you should try to fix that before upgrading the configuration. If there are daemons restarting, errors in the /var/log log files, or it doesn't stay in standby mode with the peer, you could open a case with F5 Support and ask them to help you diagnose the issues before upgrading.
Aaron