Hi Andy,
When it comes to performance related items, typically the issue comes from somewhere further down the disk storage stack as Storage Foundation does not control or manage I/O.
You mentioned that this began 3 weeks ago. Did anything change before then on the servers or the environments? Any patches or updates?
Also, you mentioned that the disks are reporting as "misaligned". I am not familiar with this term. Exactly what is reporting this?
Also, you mentioned that VVR is disabled/broken. Can you be a little more specific? What state is replication in? In VEA > Replication Network, what do you see? Make sure and connect to both servers within VEA when checking this.
-Mike