Since you have gotten www and the webserver working, you can start with the PHP stuff.
http://buffalo.nas-central.org/wiki/Category:LS-WXL#Gain_Root_Access
What they mean by adding that line to get root is this:
Go to the newly created shared folder called www, and find the index.php file. Replace the contents of this file with the PHP script in item 8. You can use a text editor. Since I am on a mac i used Tomato. I think notepad will do too.
Now to execute this script, you need to go to your webbrowser and point to this index.php. You need to enter the NAS IP address followed by the port number and the file name. In this case index.php.
You have now achieved root access.
As I mentioned previously, I am on a mac. So to gain ssh access, I used terminal. I am not sure how this works on a windows machine.
In terminal ssh to the ipaddress of your NAS. Looks like:
ssh root@ipaddress
If you get prompted for a password just press enter. You should now have access to your NAS via SSH.
go to the specified directory via: cd /etc/init.d
Now you need to edit the twonky.sh file. For this I used vi editor. Check out http://www.cs.colostate.edu/helpdocs/vi.html for the commands.
Roughly you will need to open twonky.sh with vi. Scroll to line 250 and insert # before this line. Save the file and you are done. Exit from vi, exit from terminal.
Now just make sure you do not click on update DTCP-IP in the Linkstation Media server settings.
Now you should be running utorrent and your mediaserver won't bugout after a restart. Hope this helps. I am not very good at writing instructions. :)