It's not there 2 times. It just includes a deeper directory structure. I realize it's not the normal structure for my themes but I didn't port that theme Jzky did. I'm just mirroring it because I did the red port and the blue port is an offshoot of that. There I repacked it again for ya with my normal structure.
Files changed from the version you have are:
Most likely you've made some changes to the header.html to create your custom header. Those changes will need to be redone with the new header.html You'll see the difference once you open it. Nothing major just some css work and ripping out some hardcoded html.