When I did a fresh install on a new 4000D with a 3640 I had to do the 3.1 installation, first, then install 3.9. I had a problem with the CD filesystem if I tried to install 3.9 directly.
Now, I was having problems installing 3.9 directly from an emergency boot floppy. I cannot recall the error but I have a thread here which describes my pain. I want to say I eventually got it to work by using a different CD, but I cannot recall.
I might try again over the weekend. It does not take long at all.
