Hi Jim,
it is possible that these yellow VMs have a big Guest OS Kernel wait maybe because of the problems with array. But this is just a long shot. Could you check the performance Tab of each VM and provide us with CPU Usage (%) and CPU Ready ticked on at least one VM? Or ideally a screenshot of esxtop for the host that has the most yellow bars visible? (the more screenshots from different hosts the merrier) - we could see what happens there. Also the storage information from the ESXtop would be nice (u and v keys). For more information about how to access & use esxtop, please see this great post: ESXTOP - Yellow Bricks
Congratulations on making further progress on this case. Anyways, to me it still seems that the VMs are being oversubscribed, so please check what processes are chugging away the most of resources so we have more data to work with. Process Explorer from System Internals is great tool to do this.
Cheers!