Well, considering these were probably not manufactured in the millions, and that's at least a 4-layer board (considering the BGA chips there), i'd say there's a chance that those bodge-wires could be straight from the factory. It must've been cheaper to correct a couple issues with some wires, than re-spin entire batches of boards...
And anyway, who else would know what signal comes out at the STP-N5(?) test-pad, for example?
Just wait for the new muxes, install those, and then see if the thing comes back to life. If it does, great. In case it doesn't, THEN it might be worth questioning those bodge-wires.