You have a good vision for the server environment, but I'm not sure if there is a simple way to accomplish it all.
I currently manage a version 9 SR7 environment like the one you described in STEP 1. The 2 servers are identically spec'd, with one operating as the Production Web Server and the other running Publisher and UAT Web Server.
Step1: Unless you have minimal load and server requirements, I would avoid VMs. Publisher consumes as much CPU as it can, and QWS consumes huge amounts of RAM. Together they would probably impact others servers on the VM.
Step2: We are currently using QlikView Web Server without difficulty.
Step3: I'm not aware of a QlikView change management repository.
Step4: The servers are spec'd the same to provide some level of DR redundancy. Also, the storage of documents on the SAN simplifies their distribution and access from both servers.
Step5: I know v10 has improved the granularity of the management console, but your request sounds beyond to current functionality. Any solution would need to be a kludge on your part.