Usual culprits are:
1 - RTL8111/8168/8411 NIC. You don't have one

Nope. Eight ports of Intel i210 PCIe Ethernet using igb driver which is known to be solid.

2 - Proxy/Disk speed

No proxy services are in use. Can't even find any proxy settings or references so those modules are likely not installed. Can you give me a clue of what I'm looking for to verify? All I have under Gateway is "Intrusion Protection".

3 - IDS/IPS

Wait, IDS/IPS suck? Why did I buy ClearOS then when I could just put up a skinny Linux box with locked down firewalld rulesets?
Result: Turning off IDS and IPS did not change the iperf3 benchmark results. Outbound from ClearOS goes wire speed, Inbound to ClearOS ~70Kbit.

4 - Bandwidth/QoS

/etc/clearos/qos.conf has QOS_ENABLE="off". There is no QOS_ENABLE_IFB entry.

5 - PPPoE on the WAN

Not using PPPOE. Just regular old Ethernet. ISP provides metro area Ethernet as a Cat5 cable and ipaddr/netmask.