You could use SysInternals RegMon and FileMon (now owned and dist by MS) to see exactly what is modified by the Java installer. I believe there will be a number of reg entries that you will want to create. Products like WISE installer, for example, also use this sort of approach under the hood to repackage product installations (e.g. as MSI).
Please be careful since there are also some dynamic decisions made by the installer which may affect what gets installed (e.g. on XP v.s. W2K3 server). I was bitten by this once regarding installed codepages. I do not recall the precise details, but the effect was that a codepage file was missing in my embedded JRE + JDK (legally redistributable portion only). This caused a very bizarre and seemingly nonsensical runtime error in my code. It goes without saying that the same applies to Server v.s. client JVM DLLs.
