thomas, couple of things that stand out to me. first, just because the battery "bought it from apple so its not done" does not mean that it won't fail. Always remember that these batteries do a lot more than just store energy. You said you replaced the battery and that it then charged. I definitely would be looking at getting a new one, again. The other thing I am unsure about is your statement about the "charger was making clicking sounds" you should definitely try to either replace the charger or try to charge your phone with a different charger. Next thing, yes it could be the dock connector. Since you already cleaned it, I also make the assumption that you checked for bend or broken pins as well. If after you installed a new battery and tried a new charger, it should still not charge, you can replace the dock connector, using [guide|1546|this guide.] You do have fuses on the logic board, there are actually two that could be giving you trouble, check the attached image to find your fuses and check those with a multimeter. Last but not least, you may have issues with your PMIC, which would require either a reflow or a reball of the IC. Hope this helps, good luck.
[image|254602|align=left]