I am currently running two CCR1016 routers with an Aviat WTM4100 microwave link in between. I run OSPF on the network. The issue I am having is intermittent spikes of latency. The microwave links are sub-millisecond latency and even pinging the radio directly connected to the router the latency will jump up to 10 or 15ms intermittently. Less that 10Mbps traffic on the link. I have updated the router to the latest firmware 6.49.17. I cannot figure out where my issue is. Any advice?
This sounds like an MTU issue where your packets are getting fragmented due to an MTU misconfiguration, however, I do not have enough information about your links and setup to confirm this such as if you are using VLANs, have layer 2 connectivity between the two routers over the link. You may test the MTU on your link by pinging across the interface by setting the do not fragment flag to true and increasing/decreasing the payload size until you find the maximum size packet for which you will receive a reply.
You can learn more about MTU at https://help.mikrotik.com/docs/spaces/ROS/pages/21725296/MTU+in+RouterOS.