you bumped into same problems as I did, i think. have a look at the post few above yours called "eorrors in install guide?", i just made it.
In short try this:
make sure you take all contents of skyrim folder (the one that came out of zip file) and paste them into your steam skyrim folder (there will be some files that will override). Your post suggests you did what I initially did and used option to extract into ...steamapps/common/skyrim folder and that creates another skyrim folder within your skyrim folder and dumps everything there. And that's not where it all should be. All those executables should be in the same folder as tesv.exe
Secondly if you follow guide on replacing "X:/" and "X:\" it doesn't work. First of all if you use ctrl+h you end up with double path (...skyrim/skyrim...) secondly "/"and "\" are mixed up... when "X:/" than "/", when "X:\" than "\".... and guide tells us to use "\" when replacing "X:/" ... makes zero sense and doesn't work... at least didn't for me until I stopped following guide and started thinking on my own. Ill paste as spoiler contentents of my modorganizer.ini below. For the reference my install path is "D:\steam\steamapps\common\skyrim". As you wil lsee in my ini file I use / where guide says to use \ when replacing paths for X:/ and i dont have any skurim/skyrim paths that get created when using ctrl+h replacing method. You could just copy paste my whole ini file and go manually use ctrl+f to to look for "D:" and replace all "D:" with your path start "C:\Program Files (x86)"