Ah, I found it working this morning.

I hadn't modified any of the base files, since I had done a fresh install of the base game prior to trying to install kingdoms. Its just that the patch somehow took six hours to complete. I had started trying to patch it again last night, then went to eat dinner and forgot about it. When I woke up this morning it had patched the game up to 1.3 and just had to install kingdoms, which only took 10-15minutes.

I'm not sure why it took that long to finish patching, but everything seems to be in working order. Thank you for your advice though.