Hi guys brand new here . Anyways to get right to it . I started playing guitar in April of 2010 but sadly I picked up some bad habits and so I am restarting from scratch but I have run into some problems regarding my technique.

Whenever I try to put my thumb on back of the neck for some reason it will start to naturally slide up and reach top of the neck . Also I tried playing a C major and keep my thumb square on the neck but not only did I feel a lot of tension in my thumb and I was trying not to put any pressure on the thumb.

As for my fingers I can put my middle and ring finger square on the fret board as soon as I put down my Index finger it won't stay perpendicular on the B string 1 fret and on top of that I can't raise it high enough to clear the the string and I'll end up feeling awkward.

Could it be that my fingers are too small . I have tried doing finger exercises to try and make them more flexible.

Also when i have tried holding my guitar my left palm seems to close to the neck and I have tried lowering my fingers and keep my thumb straight and not on top but it just feels too difficult and I end up having trouble fretting notes or playing a few simple chords thus not having fun.

I don't want to give up but for the last year and a half I've never been able to my holding guitar and hand techniques down. And I'm totally at the end of my leash lol.
It seems like wasted time to try to imagine what you described in your post =|
My advice would be to ask a good guitar teacher for one private lesson where you explain and show him what your struggle is, then he maybe could find your problem and tell you what to do about it!
gee thanks it looks like it was a waste of time asking for help . lol thanks I'll look elsewhere
My thumb is always over the neck. When i learned though, it was always behind the neck but it felt more natural over the neck so for chords like D,C and Am, my thumb usually wraps over and mutes the low notes.

If it feels natural, go with it. If it hurts, you're doing something wrong.
G(g)od was like: "Make you an ark of gopher wood; rooms shall you make in the ark, and shall pitch it within and without with pitch."

And i was like: "What's gopher wood?"
Your hands are probably not too small. Also your finger positioning may be partly because of your guitar. My thumb never goes over the top on my LP but they have pretty beefy necks. Ideally you want you hand to leave a little room on the bottom so your thumb shouldn't be up that high unless you have huge hands or the neck is very thin.
re-starting technique all over again is going to be awkward no matter what - even if it's better technique... you need enough time to get used to the feeling of it.

My theory on thumb position is let it go where it's comfortable... but be able to move it around to different positions as needed.
Outside of classical & jazz, I don't see too many players who keep thumb behind center 100% of the time.
That said... your thumb wandering could be effecting your fret finger problems too.

So you might wanna look at the entire fret hand as one single technique while you re-learn.
Check your wrist angles on the neck. That can seriously impact what feels comfortable (or not).

a photo of your current fret hand problems will probably get you better advice.