Hi Jake,
Sincere Apologies on the late reply. I had an alert set for a reply to this thread, but I never received it.
I believe I did find the causality of my issue. Enabling 3.0 would completely freeze the boot process, and upon reviewing my clover settings I found that USB Ownership and Injection were not checked. Enabling those I am now able to boot into the system and utilize all the USB 3.0 ports.
Thank you so much!