Hyper-V VM will not shut off, turn off, or Migrate

Have you thought about installing SP1 for Windows 2008 R2 on your host servers?  It has many fixes to Hyper-V and includes some excellent new features like thin RAM provisioning.

Further questions:
Are the integration services installed properly?
Are the event viewer logs on the host and guest VMs showing anything?
Is your cluster configured correctly?  Since you only have 2 physical servers are you using a shared disk as the quorum?

1 Yes I have S1 installed on all servers
2 I will have to checck on the integration but I am almost certain that they are installed
3 nothing is showing up in the event viewer
4 Yes the cluster is configured correctly and I am using a quorom disk.
5 The only oddity here is that I am using Virsto software that allows for IO offloading though ISCI and I am starting to think that it is too finicky. This software also allows for better use of the SAN storage but not sure if it is worth it anymore.

Virsto advertizes some tremendous efficiencies in dealing with the "IO blender" that comes from the more random IO that comes from multiple VMs.  I haven't worked with it personally.  It does add a significant layer of complexity.  If you have support you may be able to open up a ticket to have them help you troubleshoot your issue.  In our experience we've been able to pack dozens of VMs on a Hyper-V host with W2008 R2 SP1 and a SAN without significant IO issues.  This includes multiple SQL servers.  However some heavy applications using SQL, Exchange, etc. may require some extra attention:  a dedicated iSCSI NIC(s), MPIO, jumbo frames, a dedicated LUN, a dedicated controller on your SAN, splitting your IO on different SAN disk spindles, etc.

I'd suggest contacting Virsto and running your issue past them for advice.

Another option is to open up a MS Support Ticket.  They cost $265 per incident and they work with you for as long as it takes to resolve the issue.  I've used their service many times.  The last time they invested about 10 hours on a Remote Desktop / Terminal Server Farm and they did resolve the issue, which was rather complex.  When you really need to get to the bottom of things MS Support is a good option to consider.

Microsoft Paid Technical Support      800-936-5800

I suppose one of the logical approaches is to verify/troubleshoot each component in your environment individually and as a complete system:
1- Physical server config including NIC configs
2- Hyper-V config
3- Hyper-V integration components
4- Cluster config
5- iSCSI config
6- Visto setup

Another option might be to export/import the VMs in question to another Hyper-V host temporarily, or migrate them live via System Center, or migrate them with a VB script.  I have a script saved to do a live VM migration but I'd have to take a few min to find it.  That would take Virsto out of the equation for troubleshooting purposes.

That would be great and I am going to work on Exporting them out and reloading the Hyper V servers and not renewing the Virsto Software. I think that it is screwing with the services. I currently only have 8 VM's on a two node cluster and each host has 64GB of Ram, so I think I may be over complicating the needs of the environment.

The question I guess would be can I move them all onto one host, redo the second one. Import them to the newly configured host, redo the 1st one then create the cluster? Or does all VM's need to be off in order for the cluster to be created?

The servers are not SQl or Exchange but the reason for the cluster is high availability, I want to make sure that they will be up at all times. I have talked to Virsto in the past and I do believe in there product but I think that it was a little much for us. I do not have the time to concentrate just on that and the only issue I have is that you need to have a separate server that acts as a Live space. Then you have to find a Storage program out there that does ISCSI connections so that adds a separate piece to the puzzle. It would be a better solution if they had the ISCSI program to go along with there software and that way it support would be in one place. I think the issue I am having is one that is with the ISCSI connection and since it is not their program they can not help and it is a free program. I could pay for a separate program but I already pay enough for the Virsto that I feel all the components should be included with it.

FYI, if you do need to build an inexpensive SAN Microsoft has decided to make their storage server iSCSI software available for free.  It lets you turn any Windows server into an iSCSI SAN.  We use an EMC SAN but I thought you might find this interesting.  An advantage of an end to end Microsoft solution is that Microsoft Support will cover all of the pieces.

Microsoft iSCSI Software Target
http://www.microsoft.com/download/en/details.aspx?id=19867

The Microsoft iSCSI Software Target 3.3 provides storage (disks) over a TCP/IP network. It turns a computer running Windows Server into a storage device which provides shared block storage. You can use Microsoft iSCSI Software Target 3.3 to perform a variety of storage-related tasks, including the following:

•Provide shared storage for Hyper-V to enable high availability and live migration
•Consolidate storage for multiple application servers (i.e. Microsoft SQL Server or Hyper-V)
•Provide shared storage for applications hosted on a Windows failover cluster
•Enable diskless computers to boot remotely from a single operating system image using iSCSI

That would be better then what I am currently using, thank you for the info.