OS X :: Changed User Short Name And All Preferences Lost

I changed the short name of my home directory oblivious to the consequences. I have searched the internet high and low and have found a few threads already posted (including an Apple support article) that relate directly to this issue. However, although the root of the problem is the same in that I changed the short name, the outcome is slightly different and I can't restore all my preferences in the manner detailed in these articles. I have a Mac OS X 10.4.11. Here is exactly what I did and what is going on:

1. I went into Get Info. in the home directory icon in Finder.
Say the original name was john, I changed it to Fred.

2. Since then, when I open any applications such as Skype, iTunes, iCalendar etc. all of the settings have been reverted to default making it appear as if I've only bought the Mac. However all my documents and music files are still there and can be accessed normally in the newly named directory. My desktop and widgets are also fine.

3. Now when I go to Macintosh HD and click into users there are 3 things:
- The newly named home directory Fred with the house icon.
- A folder with the old home directory's name, that being john. Inside there are Documents, Library, Music and Pictures folders but only the Library folder seems to contain anything important, which I hope are all my preferences. The other three are effectively empty. Like I said I can access my music files etc. normally.
- Lastly the shared folder.

I haven't turned off or restarted my laptop because reading on threads it appears as if I can cause damage or end up not being able to access my mac. The two solutions I've found online are these: [URL]. The problem with this one for me is that I can't rename the new directory with the old name - it just won't let me. [URL]. The problem with this solution and another I found is that I think they are assuming the old directory - john - is in fact still a directory but in my case it is a folder.