#1
What I am doing at the moment is, I hear a song, I'll play the notes by ear (only the notes, no chords). Once I know which notes I am playing, I look for chords that sound like those notes. So for example let's say the notes I played were A(3string/2fret)-- E(4string/2fret) --G#(3string/1fret)-- F#(4string/4fret)-- D(4string/0fret).

The problem here is that if i just play Amaj, Emaj, G#maj, F#maj, Dmaj it does not sound like the song. My question is, did I choose the correct chords, or do I just have to change some of those chords to minor, suspended, 7th chords, etc.
#3
You most likely have to change some of them to minor, suspended, etc. They are almost no (read: very few) songs where all the chords are major chords. Also, if you choose full chords with rock/metal/funk/etc., you're going to miss the mark because there's many genres that don't use full chords like Amajor or Dminor.
#4
Remember that the notes you play may not always be the root notes of the chords. Chords have at least three notes in them. So you may as well be playing the fifth or the third of the chord. I would suggest learning some theory.
Quote by AlanHB
Just remember that there are no boring scales, just boring players.

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#5
in addition to the above suggestions...some tones do not require a "chord change" ...

if the notes are the melody..there could be many ways to "harmonize" the notes...example

take the notes...A B C...you could harmonize them (keeping the melody notes on top-the highest note of the chord)

using the keys of Am/CM

Ami7 Ami9 Ami7
Ami7 E7 E7#5
C6 G7 CM7
Ami7 Bmi7 C6

a study of theory and harmony will help you understand what you are trying to do