#1
HI, im learning to play guitar, and struggling to fit my 1,2 and 3rd fingers between the frets on an open A chord. I can fit my 2,3 and pinky in alot easier and it feels fine. Will this cause me problems in the long run ? When i use my 1,2 and 3rd fingers i get a horrible vibration noise off the fret.
#2
That may well help in the long run when it comes to barre chords. You use your 1st finger for the barre and move an A shape chord up the neck to form other chords there; very useful for those too lazy to learn "proper" chords.

*edit* As a general rule, if it sounds good it is good. There are, of course, exceptions, but it works 90% of the time.
#3
use your 2nd, 3rd and 4th. It will help you if you jump to a barre or power chord next as well.

EDIT: I'd practice what my comrade above said as well.