Performance Degradation Troubleshooting
Converting my comments to answer ....


  Total Physical RAM = 3583, Virtual = 3583, (1) 21GB, (1) 13GB, (8) 4GB, a handful of smaller ones plus 17GB proprietary file storage. The power plan is currently Balanced.


Based on your above comment, with a mere 3.5GB RAM, you are running dbs totaling the size of 65+ GB. There will be resource starvation on the database server.

Increase the RAM close enough to the size of db and change the power plan to high performance.

Then monitor your db server with sp_whoisactive or SQL-Server-First-Responder-Kit and start tuning when you have data.