Ok, i`ve made some progress, by replacing the 3.1 rom I got off Amiga Forever with one I used on an old uAE setup called kick31.rom I got a requestor asking me which os to use, I selected 3.9 and it copied files off the cd. However I now get a recoverable alert when I try to load E-UAE.
That recoverable alert seems to hit quite a few people. The solution I found was to simply cold start e-uae again. You may need to do this more than once. We think the recoverable alert is caused by afa_os which is not present on the install but is present once installed.