SQL Server High Disk Queue, Low CPU
I think best approach is try to find connections, which use most IO.

Look at open connections, see who use most IO.
Look at currently executing commands, what they wait. Would be seen some waits on latches. 
After finding who use most IO, it would be easier to make next step in investigation.

As for CLR, there are performance counters which shows quite a lot information about its behavior, so it is possible to look on it.
May be there is usage of swap on the server? Like page/sec significanly above zero? It also may cause such behavior of server.