If I remember correctly, I installed OS3.5 on my WinUAE setup copying my A3000's or A1200's workbench to my PC via my Siamese connection and then tweaking that to make my UAE "hard drive".
I had the same problem when trying to install it from CD - hang-up after hang-up. I also tried to copy the contents of the CD into a directory on my PC, but windows crashed each time it tried to copy a certain file off the OS3.5 CD (I can't remember which one it was, but I did track the litte *#@ down).
Hopefully that Cloanto site will give you a better guide.
PS. I refuse to buy OS3.9 until those cheating H&P &%^%ers pay Amiga Inc for OS3.9 and Amithlon/XP!!!