Besides the few specifics already given, human hearing is too vastly complex for us to deal with in any completeness here. First, make sure that your guitar is adjusted properly and has good strings. Buy an electronic tuner, use it and trust it. The guitar won't sound perfect to a very good ear but it will sound fine to most of us, and you can switch keys with impunity. If you don't have an electronic tuner, tune your high E to whatever is available and then find an E on every string and match it to the high E. Don't mess with harmonics.
Harmonics are perfect pitches above an equal temperament fingerboard.
Start with the electronic tuner and then adjust your tuning using your tuning pegs or by bending individual notes in a chord as you play until the sound pleases your ear. Try tuning to perfect pitches where you are going to spend most of your time in a song. The F and G chords will be fine and when you go up the neck to play lead, bend into tune . Or, play fast and no one will notice .