Will the upper pins and bushing work in the lower door hinge? I work at autozone and can onky get the uppers through there but my lower bushing is completely gone and I want to replace the pin aswell while im in there.

No, the upper is completely different.
I'm sure there is a way to order them through Auto Zone's system--unless they are so completely lame you can't.
No parts stores around me carry the upper, but they can order them in.
Worse case, order them from Rock Auto or 1AA Auto.