The inputs are fairly low impedance (up to 10k) for electromagnetic pickups, so I am not sure I'd advise to add even more load to the pickups by sending them somewhere else in parallel, though if that's going through a high-impedance input, maybe that would work? Could you not consider passing them through digitally to the outputs instead? That would add the conversion and buffering latency, but maybe that's fine for your application?
If you do want to do the analog passthrough, then you can access a copy of the signals on the 2x1 headers of the input wing, but you should not connect it to an unmodified output wing's output sockets. In that case, the signal would be "fighting" against the signal driven by the audio outputs (even if these are sending zeros). What you'd need instead is to prevent the signal coming from the Multi cape from reaching the socket headers and jack sockets. This may be done by cutting traces on the PCB (see design files here) or - much easier - cutting pins from the pin header going into the cape. Then the socket headers and the jack sockets will remain connected (i.e.: you can feed a signal into the header and get it at the jack) but there won't be any interference with the signals driven by the multi cape.
