When it comes to the quorum/witness disk (Windows 2008 and later called the disk a witness disk. Windows 2003 and earlier calls the disk a quorum disk), my advice would be to re-create the witness disk in the new location instead of migrating it. The quorum/witness disk itself should contain no data other than the cluster configuration information. Each node in the cluster will also contain a copy of this data. While there is no quorum/witness disk, the fault tolerance of the cluster is reduced, but the quorum/witness disk would be replaced before the cluster is put back into production use, so the risk is well mitigates.
The process I would use is...
1. Change the cluster to not use a quorum/witness disk and remove the quorum/witness disk from the cluster group.
2. Migrate all other LUNs as planned.
3. After the migration is completed, add a new quorum/witness disk to the cluster group and change the cluster type to use the quorum/witness disk
If you are not using SnapDrive, I *highly* recommend using it. SnapDrive will add LUNs to all nodes within the cluster and assign the specified drive letter -- without taking the cluster nodes offline. SnapDrive also allows administrators to grow LUNs without stopping clustered services.
We MS-Clustering and NetApp storage for many of our systems. If you have any additional questions, I'd be glad to help where I can.