He is having a tough time determining when I want him to move his haunches away and when I'm moving up next to his shoulder.
Do you mean that when you're at his flank he understands when you ask him to move, but not when you're up closer to his head? Sounds like you're possibly asking a bit much & stick to what's 'easier' for him for a while longer first, before *gradually* teaching him it means the same thing when you're in different positions. Horses are hyperspecific & don't generalise well, so he hasn't learned it means the same thing when 'different'.
However his mentality is to not trust humans. Which I am continuously trying to strengthen our bond. Day two of our training I was bitten twice, kicked in the wrist and he decided to jump over a panel fence when he was put up for the night.
I find it hard to explain, but in working with a 'damaged' horse I wouldn't necessarily do things differently with regard to training. Good, consistent, clear & effective training should help him gain trust & respect in you. But I would be striving to make everything as Good & positive as possible for him, as well as easy, non stressful, non confrontational. You might find learning the principles behind 'clicker training' is invaluable.
He also sounds like a possibly quite 'assertive' guy, who by 'temperament' or experience, may have more 'fight' than 'flight' about him, so needs to be handled carefully to keep that below board.
quarters he is very difficult to rein. I believe this is do to him having such an aggressive bit and people riding him who were very pushy and jerky with his mouth. I am using a chris cox snaffle bit that is very gentle
How well does he yield(respond softly & reliably with understanding) to pressure elsewhere aside from his hind quarters? I'd be spending more time making sure that was all good before riding.
I'd also ditch the bit, for now at least. If he's had so many terrible experiences with it, those associations will be really getting in the way of his learning & accepting. A snaffle is not really a 'gentle' bit, and any bit can be as harsh as the hands on the reins & training - meaning you may not be 'heavy handed' but if his training/associations is getting in the way, you may not be able to be 'light'. Get him going well in a halter, bosal, bitless bridle, which should be different enough in feel that previous experiences/associations won't get in the way so much.
Also I am trying to teach him leg cues with correct seat position
Don't blow his mind. You've only had him for 2 weeks & he's had a bad start. Start & work at where HE is at, teach him the basics first & one thing at a time, not try to do it all at once. I'd also be getting him great at yielding to light pressure where your legs will be, when you're on the ground first.
I usually work with him for an hour or so on the things you mentioned. ... I tend to put pressure on him when he loses focus and that could be causing more harm than good.
Putting pressure on him when he loses focus could indeed be a bad move. Or it could be the exactly right thing to do. Depends on the situation & his attitude. If he's worried/frightened, putting more pressure on him is not great, but being assertive if he just 'ignores' you is different.
Re the hour sessions, sounds very intense & intensive. I'd be cutting down to about a quarter of that time or less per session. Of course there's nothing to say you can't d 4 or more shorter sessions daily, or do 5 minutes 'work' & 5 minutes hand graze, groom or feed him in between 'sessions'. You'll get more 'bang for your buck' with short, easy & positive sessions rather than one long, tedious one.