1. You need to set the QVS setting of the QVWS, at QMC > System > Setup > QlikView Web Servers > QVWS@servername > AccessPoint > Server Connections. Make sure it goes to the right QVS name.
2. If you want to cluster them, make sure you are using a UNC-path as the "Document root folder" under QVS settings. Your license needs to support this too. It works to have them separated too, but they won't "cooperate" in that case.
3. No, not if machine 2 is not using it's own QMC. The configuration of the initial QMC is fine. Remember to only have one QMC per environment, otherwise you will run into conflicts.
4. If you are clustering: no, if using UNC-paths (\\servername\share\folder), yes if using local paths.
If not clustering: yes.
5. If you want to connect machine2 with machine1, it depends on your environment what you want to do. Every configuration is different, but only 1 QMC in the whole environment if they are "working together" (clustered or non-clustered).
Let me know if this helps.