I do not have your particular platform, but, in general, my experiences with port-channels is that you do not configure the ports -- you add the configuration to the port-channel irtual interface. Have you tried removing all interface config, joining them together as a port-channel, and then applying all link config info to the port-channel interfaces?
Also, most qos settings (but not all) only apply to output from an interface queue, meaning they apply in the outbound direction only. To get qos in both directions, you'd have to set qos on the switch links to the router as well as from the router to the switch.
Just had a thought, you've posted one instance of a 30 second average, what does the long term packet counts look like across each channel link?
Reason I ask, channels, I believe, preserve flow sequencing by not distributing a single flow's packets across multiple links. If correct, a short duration snapshot would show varying usage of each link. Longer term, it should balance out unless you have a couple of heavy flows that move traffic between a pair of hosts that hash out the same. (The hashing, I also believe, is deterministic. New flows with the same hash parameters will always use the same path.) If the latter situation (host pairs), some hashing methods also support using IP ports for the hash. The key is finding the method that provides the best overall distribution for your traffic, but understanding that there can still be differences in link utilization. (One of the advantages of faster links vs. channel bundles.)
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