@EOM,
To answer your question, yes, this can be done programmatically using a script/program. The method you're looking for if you're familiar with the vSphere API is ReconfigVM_Task() (it's a catch all function to perform any changes to a VirtualMachine). You have the ablity to configure both the shares and IOP limits using the new #storageIOAllocation property (http://vijava.sourceforge.net/vSphereAPIDoc/ver5/ReferenceGuide/vim.vm.device.VirtualDisk.html) introduced in vSphere 4.1 which is defined on a per virtual disk for a VM.