Have you tried following the process described in the documentation?
Here's what your files are (source: GoDaddy cert chain repo)
- gd_bundle-g2-g1.crt: Go Daddy Certificate Bundles - G2 With Cross to G1, includes Root
- gdig2.crt: Go Daddy Secure Server Certificate (Intermediate Certificate) - G2
- some_hex_string.crt: Your certificate
Before you start, you may wish to confirm what exactly all these files are from your server admin, just in case...
You will also need the private key for the wildcard cert if you want to install it on your TomCat server, unless you already have the private key (e.g. if this is a renewal). If this is a fresh install, you will definitely need the private key.
Also keep in mind that keytool is extremely unforgiving and also very dumb when it comes to error messages. It will mislead you with useless error messages like
keytool error: java.lang.Exception: Failed to establish chain from reply
What that could mean is that you need to explicitly specify key sizes and algorithms manually (see keytool help for syntax and parameters).
Practical advice: avoid keytool unless you absolutely have to, or unless you know it inside out. It will most likely drive you insane, unless you know it well. If you don't know it well or get stuck, I suggest using a 3d party Java keystore editor like KeyStore Explorer or Portecle.
Advice #2: use nginx as a reverse-proxy front end and SSL offloader for your site. SSL is much easier to implement on nginx, and it will allow your Tomcat instance to focus on application delivery, which is more than enough to keep a Tomcat instance busy with. :) Furthermore, you will be able to tweak your SSL/TLS settings to achieve a reasonable score on Qualys' SSL Labs SSL Test. In this day and age of numerous SSL vulnerabilities, this is not a bad idea... I'm not certain what the default Tomcat 6 SSL config scores on that test.