they haven't identified any auto-antibodies in ME patients yet
I think they have, but not consistently, and so far as has been announced so far, not correlating with improvement from Rituximab.
A systems approach is what I would do if I could get involved in research as a scientist. Even if an autoantibody attack is the cause, and it might be, then this approach may well identify key targets the antibodies are attacking. This would enable highly specific tests to be run to see if these targets are being attacked, with the potential to finally isolate the autoantibody.
If an autoantibody attack is not the cause, which seems more plausible, then its highly likely that its an autoinflammatory response. This might also respond to Rituximab. Such a response could be identified with a systems approach.
One serious caveat I have with such an approach though is it is highly dependent on which tissues are being examined. There are no brain biopsies for example, and if the brain chemistry turns out to be necessary to solve the puzzle then this would be missed. To be clear, I am definitely not recommending brain biopsies, and you wont see me in a line for one.