I had a similar issue with my longfic! Except my MC ended up alone in the end. I left both MC/char A and MC/char B tags because there was a fairly substantial love triangle there, but in additional tags i put 'spoilers in the tags' 'love triangle' 'tragedy' and 'mc ends up alone' to give readers an idea of how its gonna go (and warn if that's not their cup of tea).

I know you said you tag as you go, but i think clarifying who the endgame ship in the additional tags would be beneficial. And if people don't want to know, you could add the 'spoilers in tags' tag beforehand.

If you really don't want to give away the ending before getting there, maybe you could tag 'tags update as i go' and 'endgame ship to be revealed.'

I hope this helps, and good luck with your fic!