Hi Julian,
I was traveling so I wasn't following this discussion, and I am chiming in a bit late.
It sound like from your initial question that you're interested in the DAE components. If you want to output the separate DAE components there are output functions in Xyce that can do this. They are debug functions, so you'd have to compile Xyce differently to use them. At the moment, the only way to use them is to compile Xyce with debug nonlin enabled. If Xyce is compiled with that option, then they can be invoked from the netlist using ".options nonlin debuglevel=2".
With that option invoked, Xyce will output the f,q and b vectors, as well as the dFdx and dQdx matrices to files. They do this pre-assembly, so the time-differentiated q vector (i.e. dqdt) isn't included. The ordering will match that of the names vector. These functions were set up mostly to debug device models. They produce a LOT of output so they should be used carefully.
Also, I am curious about what you are doing with adjoints. I implemented the adjoint methods that are currently in Xyce a while ago. I've been aware of at least 2 external (i.e. non-Sandia) groups that have added their own adjoint methods to Xyce. There are certainly many ways in which they could be extended and/or improved that I'm aware of, but haven't had the bandwidth to pursue.
thanks,
Eric