When choosing a wandering spirit, the spells granted by that spirit are now available. However, pcgen does not update the spell list. I briefly looked at the domain handling, but it was not obvious to me how to fix this.
Per pathfinder rules (https://aonprd.com/ClassDisplay.aspx?ItemName=Shaman): Emphasis mine
Wandering Spirit (Su): At 4th level, a shaman can form a temporary bond with a spirit other than the one selected using her spirit class feature. She must make this selection each day when preparing her spells. While this feature is active, she gains the spirit ability granted by the spirit. She also adds the spells granted by that spirit to her list of spells that she can cast using spirit magic. She does not add the hexes from her wandering spirit to her list of hexes that she can choose from with the hex class feature. At 12th level, she gains the abilities listed in the greater version of her wandering spirit. At 20th level, she gains the ability listed in the true version of her wandering spirit.
I can see why this wasn’t implemented. PCGen does NOT handle changing spells well. I can easily Grant spells, but removing them is a pain. Deferring this till Formula System Phase II is implemented.
One thing I discovered in my first expirimentation is that change the DOMAIN section in acg_classes.lst so that each was a PREMULT on either the spirit or wandering spirit would then have the domain associated with the wandering spirit show up in the domain selection.
However, I would then need to go to that tab in the character selection to select that domain. That may be sort of a hackish workaround (better than nothing), but I did not test what would happen after changing the wandering spirit.