Actually, I learned something new myself, here; you can clone using the API. It's covered within the main API documentation, under Create Organization Network
https://developer.cisco.com/meraki/api-v1/#!create-organization-network
and use the copyFromNetworkId parameter
Note that I'm pretty sure you will want to configure your Azure vMX as a Hub, with all of your branches configured as Spokes, tunnelled to that Hub. In that setup, you would have no tunnels to either your DC or your Head Office. You don't need to use OSPF at the Hub vMX.
I'm pretty sure you will also want your branches (Spokes) in Routed mode, with VLANs and your Azure vMX Hub in VPN Concentrator mode.