Going to look for someone you’ve been in a relationship with doesn’t have to be stalker behaviour. It’s just messy unresolved communication.
Yami communicated poorly and gapped it, and Yuu would have been wondering whats happened to a person that’s important to him.
Thanks for the translation, glad there is still more story to go find In the LN. Hoping they end up explaining the old technology in this world and No. 6 can reunite with the other Kisaragi leaders. :)