Since you havn't invested too much in this server yet, why don't you get a copy of Xubuntu, burn it, and install to it on the server. You can then install Samba for file sharing with your other windoze boxes. You already have some experience with Ubuntu, Xubuntu is the smae system, minus Gnome and with Xfce installed. This will work just fine, and you won't have to learn the ins and outs of a new distro.
What you describe in question 2 is normal for any linux distro. If you open a konsole, go to any directory in the / area, all the files are owned by root, so unless you are root, or belong to the root group ( not recommended ) you may only be able to browse the files.
On that konsole do a su ( switch user ) and enter your root password. Then go to say /etc and run a command like 'ls -l' and you will display the permissions of the files. You will see something like this:
drwxr-xr-x 2 root root 4096 Sep 6 2006 urpmi
-rw-r--r-- 1 root root 34 Nov 4 2005 version
The first line is a directory, notice the 'd' in the first column. Notice root owns the directory and the second line ( its a file ). The wrx on the directory says root can read, write and execute in this directory. Note the file says -rw-. This means root can read and write the file, but not execute it. The next three columns are for group, and the last three are for 'other'. Other can only read the file, no write no execute. You are 'other' unless you log as root.
Hope this explains what is going on...