There are two different versions of the story with Indis. In one, she is identified as Ingwë's sister. In the other, she is the daughter of Ingwë's (unnamed) sister. In either case, Ingwë definitely has a sister. As for what happens to Imin, we have some options. He or his wife could be one of the elves stolen by Melkor, and thus some combination of death/grief makes him step down. OR, he could have interest in other things, and leaves leadership to others of the Vanyar. I don't think we have to be too worried about making Ingwë one of the oldest elves at Cuivienen. He is merely the leader amongst his people, for whatever reason. We could make Ingwë the son of Imin.
Elwë is of course clearly not one of the unbegotten, as he has brothers and no wife.
I don't want to go too far with incorporating this story, but perhaps having three different 'settlements' along the lakeshore at Cuivienen with the three different groups divvied up accordingly. The Vanyar are the smallest group, the two larger groups are a mixture of Noldor/Avari and Teleri/Sindar/Nandor/Avari.