If you're using the steam version of Skyrim for Windows, there's a very simple way to install Perfectly Modded and it's by using something called a Symbolic Link.
This was tested with windows 7 and version 4.4, but should work for 4.3 and other Windows versions as well.
A - INSTALL SKRYIM
1. Install Skyrim to any location. I would highly suggest making a steam backup before doing any modding as this allows you to quickly and easily revert to an unmodded game.
2. Download Perfectly Modded, and use 7zip to extract it into the Skyrim folder.
B - CREATE THE X PARTITION
3. Open Disk Management.
4. Select the drive that Skyrim is installed to. Right click and choose "Shrink Volume".
5. When the new window appears (it may take a minute), change the "enter the amount of space to shrink in mb" value to 10 and then click 'Shrink'.
6. Wait. When it's finished, you'll see a box that says "10 MB Unallocated". Left click it and choose "new simple volume".
7. Hit next twice. Change the assigned drive letter to X, name the drive Skyrim and hit next some more. Hit finish.
8. Now you have an itty bitty X drive. Awesome.
C - CREATE THE LINK
9. Open up the command prompt as an administrator.
10. Type the following, making sure that the italic path points to where you installed Skyrim in step one.
mklink /D X:\Skyrim C:\Steam\steamapps\common\Skyrim
11. Hit enter. You're done.
You will still need to make sure all addons are checked off within Mod Organizer and that you adjusted the required settings in the NVidia control panel, but you will no longer need to modify any paths in modorganizer.ini.
1. This method eliminates most of the possible user error that can arise when using a steam version of the game. Here, the only possible error you could make is typing the command prompt command incorrectly (a typo, or defining an incorrect location for your game installation.)
2. Your partition can be as large or as small as you want it, as nothing is actually going to be stored there. 10 is a nice round number, and it seems like the minimum is 8MB.
3. Symlinks work in Windows Vista forward. If Windows 10 won't allow you to make one, practice your GoogleFu. I don't use W10 and therefore cannot help you.
4. You must open the command prompt as an administrator in windows vista/7. But, turning off UAC might remove this requirement.
5. To paste within the command prompt, use the context menu.
Why it Works
A symbolic link functions sort of like a shortcut. According to Microsoft....
"A symlink is essentially a pointer to a file or folder located elsewhere, consumes little space and is very fast to create (compared to copying a file and its contents)."
We created the x:\skyrim folder that the mod wants in order to function correctly, but we didn't put the game there. Instead, we told windows that anything that points to x:\skyrim is actually found somewhere else. This is why you don't need to modify any paths. When Mod Organizer looks for something in X:\Skyrim, windows will automatically know to look in your steam installation folder to find the file.