To download the fixed prealpha stuff, first download this:
http://dl.dropbox.com/u/96184966/Katawa%20Shoujo%20Prerelease.rar
This is the base for the prealpha, with fixed menus and such.
Unzip it to it's own folder, and, if you are computer illiterate, make a backup.
Next, download these patches, in this order:
http://dl.dropbox.com/u/96184966/KSALPHASCRIPTSPATCH.rar
This patch fixed Emi and Shizune's routes. Download and install it FIRST.
http://dl.dropbox.com/u/96184966/Rin%2BHanaLilly%2BHanako%20fixes.zip
This one fixes Rin's, adds the unused HanaLilly act 2 (In which both Lilly and Hanako love you at the same time like two hallways only without people bitching about it every few days or so), and adds Alphabro's Hanako fix. Apply it AFTER the first patch.
 
To apply the patches, unzip the files, and paste the folders inside into the prealpha folder, replacing any existing files.