Armature pose position is different orientation from initial layout in edit mode, and automatic weighting problem So I've been trying to fix my bone axes so that my arms are bending correctly and I've been running into a lot of pitfalls. This is my third rig for this mesh so far so I'm hoping that somebody can help me. 

I essentially have two problems that are going on. The first is that my hand is rotating to a weird position when I go from edit mode to pose mode and enable the pose position. 


I've tried changing the main hand bone's axis positions but there seems to be no luck with that, as well as no way to apply the rest position to the pose position. This problem may extend further up the arm, but I would like to keep my arm's axis positions so that they can bend correctly.

The second problem I'm having, which is further up the arm, is that the upper arm bone is creating a deformation when automatic weighting is applied. 

I think this is based on the axis orientation again, but like I said I need the axes on the arms to be Global Z Positive. 

It's worth noting here that axes seem to be different when switching from edit mode to pose mode. I'm posting a link to my blend file so you can see what I'm talking about.

http://pasteall.org/blend/index.php?id=50168

I would really appreciate it if someone could help me, I'm a beginner still and just want to move past this part as it has become a nightmare to fix.
In the IK constraint of your lower arm, you have to correct your Pole Angle to something like -180°. You often have to make this kind of correction after you've parented. I see you already changed to -90° but this was not enough.

I guess there are some other corrections to do. Personnaly I would parent the hand to the handle, and deparent the pole target from the handle, and make something simpler for the foot, etc... but maybe I miss something   ;)