Ok, so i had to remove the doors to deal some rust and to prepare for paint. I've cleaned up the
hinges but forgot to mark which went where. Do they go back in with the C clips on top or bottom?

don't know what a c clip is but if you describe it I can go look at mine and even take a pic if you need

ok went and looked at mine .... hinges look pretty straight forward ... there is a "clip" ..sorta c shaped that prevents the door from opening too far.... on my car it can only go on the top hinge ... it is attached with 2 bolts and there are only holes at the top hinge for this clip to be attached ... no holes on or near the bottom hinge that would allow attachment of said clip ..... hope that helps .... and if that is the clip you are talking about and by top or bottom you mean inside or outside ??? mine are inside the hole that the hinge goes into .... let me know if you want a pic

mine has circlips on both ends of the hinge pin.

oh duh ... c clips ... always called them jesus clips .... mine has them top and bottom also .. boy do I feel dumb