Got some great feedback from the community about fixing our EMI problem. In summary:
- Try Lifting the USB’s ground on one side or the other.
- The last faraday cage we use was likely steel, which can have enough resistance to pass radio frequency. Try aluminum faraday cage.
- Use USB cable with ferrite bead like this one Dave purchased:
I have an electronics chassis I’ve recycled to try as the next faraday cage:
Prometheus Fusion Perfection 
Have you thought about getting an old (used cheap) pawnshp microwave? It’s a purpose built faraday cage to keep microwaves in.
Just another thought:
http://www.bb-elec.com/product.asp?sku=UISOHUB4
Opto isolation means that there is no electrical connection between the various USB devices and computers. This should help your EMI problems.
Unfortunately at 400$ this part isn’t cheap. Lifting the grounds is certainly more cost effective.