well, I am still not sure what I did wrong, but I found a mel script that allows you to correct the direction of your joint orients, and now my joint orients are all pointing in their correct direction. You can find it right here at SimplyMaya's download page which it is called ak_fixJointOrient. It is a pretty cool script cause all you have to do is click on the root bone and then use the mel script which does the rest for you.