Okay, I learned this the hard way. When you export from makehuman the default for the character is the "A" pose. If you try to change the T-Pose and import into blender using MHX2, the bones are kinda screwed, looks like the axis are flipped. Tried to fix it with no luck, so I chose the simpler method.

My solution is to change the A-pose to the T-pose and set that as the rest-pose. I think it should work, have to try and parent the clothes next and see how that works.