I'm not having this problem but I don't have quite as much going on either. Before any other trouble shooting, power off your modem and router. Give it about 2 minutes and turn the modem back on. Once its fully booted, power on the router and see if the problem is corrected.
If you're still having problems I would recommend turning off everything you mentioned in your post; jumbo frames, link aggression, ipv6 and disconnect the 2 switches. Start turning the features back on one by one then adding the switches one by one. I believe the switches you're using are managed? If so, double check the settings on them, update their firmware, etc.