Am I explaining this poorly ?
You're doing fine.
@Rbcc has a bad habit of rewriting your examples by changing the arguments, or running commands out of order.
Garlin and hsehes do you follow ?
I would refer you to this WinPE flowchart:
Windows PE startup sequence explained
Some problems can be avoided by using boot.wim index #2 (no Setup), and completely replacing what Setup normally does with your own script. You're basically almost there.
Replacing Setup using boot.wim (index 1):
Write a startnet.cmd which calls:
1. wpeinit
2. Create and run a diskpart script
3. DISM /apply-image to C:\
4. bcdboot /s C:\Windows
5. Copy answer file from media to C:\Windows\Panther (edit file to assume you're starting at specialize pass, skipping WinPE pass)
5. shutdown /r (reboot into specialize pass)
winpeshl.ini is generally used to call higher-level deployment tools. While you can use it to run a script, you might as well leave winpesh.ini empty and have winpeshl fall back to run startnet.cmd.
The only difference is it's assumed startnet.cmd will run wpeinit, and winpeshl doesn't run wpeinit (because the MDT and SCCM deployment tools will handle their own initialization steps).