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 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:\!
  1. 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
  1. Unmount WIM:
Dism /unmount-Wim /MountDir:d:\! /Commit

Another easier way is to add a user script in Boot Disk Creator while preparing bootable media. This script is automatically launched when WinPE is loading.