There are times even with the tool your trouble will be evasive. My last experience on a 311 with similar trouble ended up being a burnt wire right at the LB coil terminal. After stripping the lead back and reattaching it, a slow march through the controller with a screw driver revealed several terminals loose on a number of relays. And no brake switch on that unit either, but a brake board, so check the molex connector.
The faults you see with the tool will be a good help too, and be sure to view/record/clear the fault logs after each visit.