Thanks for the responses.
I have been still learning the joint orientation and proper placement and such. When I think anatomically, I can figure it out, but I realize one cannot just simple place joints all haphazardly to follow characters modeled out of the normal A or T pose. We have to draw a straight chain, then rotate from the root only, or at least that's what i was taught and you can only rotate on 1 axis on the rest of them.
I'm still having issues though with using the joint orient tool. i can't always get the danged joint to orient the way I think they should and I've gone through all the settings and blah, still not right. I've tried to manually adjust them with component mode and that doesn't work at all; the joint doesn't move. Very frustrating.