I think I will not get any specific help
.
You need someone who has the specific hardware as you, and who has also made a 3.9 ERD. Surely you can't be alone, but the people who have may not be visiting this forum.
FYI I don't think your problem is a "3.9 problem". You're trying to make a bootdisk that supports the second IDE header on the FastATA card. You need it to contain the necessary applications/commands to activate said header. This could be a bootdisk for anything, really, it doesn't have to be specifically 3.9. You might try googling the process to make a bootdisk for FastATA, rather than anything 3.9 specific. Even just a regular old 3.1 floppy with FastATA support, etc. Make sense?