Packaging JRE/plug-in with Mozilla & our app... is JRE installer required?

We distribute a version of our application as a standalone implementation of our web application. We use an applet to act as a wrapper of our application server, proxying request/responses through JavaScript/applet instead of HTTP/servlet.
Right now we package the installer for our standalone application so that it installs JRE 1.3.1_01 using the standard installer, then installs the application. When the user wants to run the application, he opens a HTML page in IE 5.5 or IE 6 referencing the applet. From here the application runs just like it runs in the server-based mode.
The problem with this model is our dependency on the target system having the correct browser. I would like to package Mozilla and the JRE with the application, thus giving us more control over the installation.
Ideally, I would like to have an installer that simply creates a directory with our application, a dedicated copy of Mozilla, and a dedicated copy the JRE. That way we could custom configure Mozilla to contain NP*.DLL in the bin/plugins directory, and have a custom policy file in the JRE. Does the JRE installer do anything 'special,' such as create registry entries that the plug-in must reference to run? Does anyone have similar experience with doing this?
Thanks!

I'm actually trying to do the same thing I've been wondering what the best way is to package the JRE in this case. Is there a way to install the JRE without using the installer and just copy the files where we need to put them? I am using Phoenix, a mozilla fork, that does not have the plugins folder updated with the proper java plugins when the JRE is installed, we have to manually copy the plugins that got installed into the Mozilla folder. Please let me know if you found anything.
Thanx.

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