Ok, what you want to do is copy the existing files to a folder, call it mybackup or something like that.
Unzip the files for a fresh install on your harddrive and copy the zcinstall folder to your store's directory. That folder might still be there if you haven't deleted it from the first installation.
by running the install script you'll be replacing the files anyway. Just so you know why you want to backup your existing files.
Also if you've made any changes to the payment modules make sure you write those down.
Have you added products to the database? If so you'll want to back the database up as well.
What is the actual problem? Maybe we can avoid a reinstall.