I'm not sure what region you're interested in visiting, but my dojo essentially has an uchideshi position. I'm not sure if there is room for another shrine assistant or not, but at Tsubaki America Jinja the shrine assistants do train in Aikido, and so far as I know, tend to live in the kaikan as well.
I imagine it's not exactly the same as most other Aikido uchideshi positions in that it's a Shinto shrine, but from what I understand (and someone please correct me if I'm wrong) it's pretty similar in nature.
Who would I contact about the possibility of a shrine assistant opening? Is there a fee to train, live, and eat, or is all that provided in exchange for work?