If I can use WinUAE to make a working IDE drive and then just drop it into the 4000 that would be perfect. I've never used WinUAE though so it would be a learning experience.
This is exactly what I had to do. I had a blank IDE HD, no 15Khz monitor and a bad 3.1 Install floppy. I purchased a cheap IDE/SATA to USB cable with power supply that allowed me to plug in the IDE drive to a USB port on my primary PC (no IDE, it's all SATA internally). Configured a WinUAE setup to emulate a basic A4000 (but with JIT and Fastest possible checked) and added the HD "Add Hard Drive" and configured it as A4000 IDE unit 0. Got 3.1 installed, IDEfix97 for my CDrom and then installed OS 3.9.
I keep that configuration around as I've done a few things that screwed up the boot and had to move the drive back from my A4000 to WinUAE to make corrections. Relying on DblNTSC/PAL or Multiscan is a pain if the boot doesn't go smoothly as you see no error messages, requestors, etc...to know what's going on.