TheMonkofDestiny: The Lone Gunmen lasted a season on its own and the title characters got a tearful sendoff in a late season X-Files episode (not to discount the reappearance of one in the later restarted seasons). The focus of the show was less on the paranormal and more on the conspiracy theory end of things. It had its stinkers as far as episodes go but in general was better than a significant chunk of certain late seasons of the X-Files combined.
The pilot episode was really good, but other than that the show leaned way, waaay to much into comedy. It was a damn waste of potential, because the couple of Lone Gunmen focused episodes of the X-Files, especially Unusual Suspects, were really great.
Anyway, there's plenty of X-Files-ish shows out there, both made before and after (obviously the latter cathegory is broader) but I can't think of nothing that would quite fit the description.
Eerie Indiana is about two kids not teachers, and has no female lead.
The Infinite Worlds of H. G. Wells definately doesn't fit the episodes described :P
Kolchak the Night Stalker has no female lead and is very clearly not a 90s show.
The Middleman is definately more sci-fi than paranormal, and none of the episodes fit.
Shadow Chasers has no female lead and is from the 80s
I don't know... how about Baywatch Nights? Yeah, the spin off with Hasselhoff playing detective. I never watched any of it, but supposedly in the second season they went full X-Files and had lots of paranormal cases.