Geez Kyrvias
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Tis the act of bringing back to life a fairly deadish thread. In this case, its perfectly justifiable since there wasn't a final answer to the problem given.
Having researched it more this morning on the chosen of mystra forums, I think the solution should lie with ensuring that one speaks and meets with CuChoineach first. When I first tried making it to the citadel, he strangely disappeared after I declined him joining. I never tried having him in my party, but I'm not sure if that's necessary. Shall confirm it hopefully later on today, when I get time to test it.