Hi TomBrady5Rings,
Yes and yes 😉
For your first question: Can you use Orchestrator to access the guest OS and run commands or scripts? Yes of course! You can use the already included library workflows in orchestrator (just browse within the Library section and you will easily find them) or you can use the Guest Script Manager Package which handles a lot of errors, traps and other things which will make your life way easier https://communities.vmware.com/docs/DOC-25474. Otherwise you can add your scripts and commands to the Customization Specification and they will get executed automatically, but I'm not sure this will work with your scripts cause it's a bit limited.
Second question: Store a VM in a specific datastore? Yes of course! Orchestrator gives you nearly unlimited options and you can do whatever you are able to script in vRO. See Sort Datastores Action and Sample workflow as an example.
Cheers, and enjoy vRO coding,
Chris