Adding in your unprocessed -> unrefined -> refined fuel chain, switching from unrefined to refined might require a purge cycle. I'm reminded of my coffee maker's self-cleaning cycle requiring vinegar water. One interesting and simple approach might be as follows:
Given a fuel purification plant capable of processing x amount of fuel in h hours:
1) Unprocessed fuel -> unrefined fuel = h hours and produces x fuel.
2) Unrefined -> refined fuel = h hours and produces x fuel.
3) refined fuel -> purge = h hours for x fuel (fuel is recycled).
Your engineering crew would reconfigure the fuel purification plant for each process type.
The economic aspects could be addressed by not only considering the value of the time and the maintenance of the purification plant, with the possible addition of requiring filtration materials to be purchased every so often.
What's the difference between unprocessed and unrefined fuel? Wouldn't jump fuel need to be "processed" anyway? The starport codes say nothing about unprocessed fuel, only about refined (A, B, C+) and unrefined (C-, D, possibly E).