There's nothing magical about a SAN that means it's not the problem. In fact, it's very likely it is the SAN, a misconfigured SAN.

Check the throughput you're getting from the sAN (google, there's detailed docs on that), chat with your SAN admin, check the SAN's performance.

As for queries:

https://www.simple-talk.com/sql/performance/finding-the-causes-of-poor-performance-in-sql-server,-part-1/

https://www.simple-talk.com/sql/performance/finding-the-causes-of-poor-performance-in-sql-server,-part-2/