If the two keyboards are programmable (without requiring a special driver) then in general you should be able to program each one of them to have different keys and things should just work. USB hubs could mess things up though.
As an alternative to the Kinesis Freestyle, you could get a Goldtouch. Their website is now ruled by business cats, so it is easier to check out the different models on eBay. The two parts are not entirely separated: instead there is a lockable ball joint.
I had intended to build my ErgoDox for pretty cheap: Buy only the PCBs in the group buy, reuse switches and caps scavenged from keyboards I had got for a bargain, build my own case and use PCB-mounted switches without a plate.
It turned out more expensive than I had planned because of import tax on the PCBs and because to get my layout I had to custom-order a set of plates anyway.
These days though there are options for the PCB and other parts both in Europe and in the US, so import tax is not a problem.
