So i found Jacobstown and liked it a little to much i whipped out all the muties im wondering am i able to live here or will they respawn?

Fast travel somewhere else, like Novac, [wait] three ingame days, 72 hours, travel back and see if they respawned of not.

None of the named Super Mutants will respawn - if you didn't do Lily's companion quest, you won't be able to get that.

Also, assuming you killed Dr. Henry inside the lodge, you won't be able to complete Rex's or Arcade Gannon's companion quests if you didn't do them yet.