The heroine had short, blue hair and looked kind of like Rei Ayanami. Can't remember the name for the like of me and I'm 50/50 on if it had an anime of not. It had a classic style to that Era, not realistic. Looked pretty shounen.
Found it by pure chance as an auto rec for another manga I checked on MAL. I had (kinda) gotten the date wrong, it started in 97 and ended in 2016. Sadly was never fully translated like I'd hoped...