You can clean out the apt folder and clean out your temp files stored in
/tmp of the root directory. You can clean apt from the commandline with sudo
apt-get clean. You will need to use Nautilus file manager as root to clean
the tmp folder. Alt+F2 and type gksu nautilus in the box that pops up. You
can also issue the same command from a terminal window.

This only a short term solution to your problem. You should consider
installing Ubuntu in its own partition and dual boot. I consider WUBI as
only a way of trying Ubuntu and not a permanent way of installing it. It is
better than running from a Live CS, but as good as installing it on the hard
drive on its own partition.