Tools to diagnose QOS issues?

Well - some good gear there, and no obvious problems jumping out at me. PfSense has all the tools you’ll need built right in to it (or installable). Plus, instead of QoS, it has “traffic shaping”. It doesn’t do any SIP ALG (by default) so no worries there.

So you can use these tools https://doc.pfsense.org/index.php/How_can_I_monitor_bandwidth_usage to find out what’s going through your connection and then, if necessary, tame the beast with some shaping:

https://doc.pfsense.org/index.php/Traffic_Shaping_Guide
https://forum.pfsense.org/index.php?board=26.0