Hey Tim,
Hope things are going well for you and the team. Here's some additional insight.
The CleanUp step that comes with WMX has three arguments: /v /m /a. These are all optional and represent the cleanup of the job version, the mxd, and the attachments. You could have three separate cleanup steps that removes each of these items separately if you wanted to.
It is important to be careful with using the VersionExists step. This step does not actually look and see if there is a database version in your Data Workspace. Instead, it looks at the WMX tables in order to determine if WMX is aware of a Job Version. If you delete a job's version using the CleanUp step, WMX will automatically become aware that the Job's Version no longer exists. However, if you delete the Job Version using ArcCatalog, WMX is not aware and the VersionExists steps will still return 'True'.
So far as closing jobs is concerned, there is a WMX System Setting to automatically close jobs when the workflow is complete. This is set on by default:
[ATTACH=CONFIG]11228[/ATTACH]
Best,
Jeremy