Are all the ports on the new AMD mainboards USB4?
No, only the top 2 are.
Will the other two ports that aren’t USB4 affect the performance of any of the modules?
I think the only limitations with the others would be eGPU support on the bottom two and display output on the lower right port. Pretty sure the cards all just use USB3.2 otherwise
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Alright 
. Thanks both of you!