Update: Trying to get back into Amiga, got the HDDs out of my 4000. The master drive was about 145 MB, slave about 500 MB.
How exactly do I go about installing a new OS through WinUAE, again? My modern PC won't recognize the drives.
Boot into Windows.
MAKE SURE YOU RUN WINUAE AS AN ADMINISTRATOR (sorry for the caps, but this is essential or you can't mount the card as an Amiga drive - the option will be grayed out).
Put your CF card in your PC's removable reader
In your UAE prefs, mount the CF card as an Amiga drive and boot into your regular HDF file or Workbench folder.
Format/Partition the CF card using Toolbox as if it was a real hard drive* (make sure you make it bootable)
Copy your files onto the CF card
Put CF card in real Amiga and boot.
*I've had trouble in the past formatting some CF Cards in WinUAE where the Amiga will recognise them. I discovered that using the updated Toolbox in Amiga Forever's "AMigaSYS" Workbench option works every time.