Are you quite sure about the matching config?
I´ve done the same thing with OS3.9, and it works.
Maybe you´ve installed UAE P96?
Give it a second look over, and try to shortcut booting by going into early startup menu, and see if you can access the CF card from there, and from CLI after a "boot with no startup sequance".
My two cents
-- EDIT:
Didn´t read your second posting good enough, okay. You seem to have setpatch run to patch it to new KS (3.5).
Try diabling all modules to the setpatch (NOROMUPDATES) and then see if it boots.
Then, secondly bring them back one at a time.
Using the editor witout WB loaded can be a pain (it neets lots of stuff, and won´t work well with "no startup sequence" - so try getting a simpler editor for debugging)
