Is there a UnityMTA directory under Commserver? This is the directory where all outside caller messages will travel through before heading to the Exchange companion server selected during configuration setup... as opposed to internal messages (subscriber to subscriber messages) which originate from the sender's inbox. I've never seen that UnityMTA directory missing error... Unity will create the directory on the fly if it's missing (the directory it uses is in the registry). If you determine it's missing, make sure we're able to create directories on that partition.
3.1 what? 3.1(2), 3.1(3)? I ask because there were some fixes in the UMR (the guy that uses the UnityMTA directory) along the way in 3.1(x)...
I'm not sure an uninstall and reinstall is really the answer here... there is an Uninstall tool that cleans the system of Unity files including dropping the SQL database and the like. It ships with Unity under the \utilities\ directory but you can always download the latest version from CCO Utilities page or from AnswerMonkey.net here:
Are you getting this error “Installer User Interface Mode Not Supported. The installer cannot run in this UI mode. To specify the interface mode, use the -i command-line option, followed by the UI mode identifier. The value UI mode identifiers...
The below trick might come handy when you have to add a new node to a cluster but you don't have or is unsure of the security password for the publisher. This procedure has been around for ages.
1) Login into the CLI of the Publisher.