We are using a WinPE environment that is booted into via PXE. Is there a way to copy registry information and files into the WIM file that we boot from, so the applications are already installed and registered? Or will I need to script the installation and registration to occur each time we boot into WinPE?

Customizing WIM is a complex task, however it can be done. You may find a documentation from Microsoft on Windows AIK (on how you can create, modify and customize WIM).

To do it, run in “Windows PE console” something like this:

  1. Mount WIM:
          Dism /Mount-Wim /WimFile:D:\ABoot\iso\sources\boot.wim /index:1 /MountDir:D:\!
  2. Attach Registry from a file to your local registry, add your values, unload registry:
          reg load HKLM\my D:\!\windows\system32\config\software
          reg add "HKLM\my\Microsoft\Windows NT\CurrentVersion\Fonts" /v "Courier New (TrueType)" /t REG_SZ /d cour.ttf
          reg unload HKLM\my
  3. Unmount WIM:
          Dism /unmount-Wim /MountDir:d:\! /Commit

Another and an easy way is to add user’s script in Boot Disk Creator while preparing bootable media, This script is automatically launched when WinPE is loading. This is how to do this:

     Loading Boot Disk User Scripts