Installing OS 3.9, please help.

[mfilos]

What about Workbench 3.1? Does it work just fine?
It seems like the SetPatch is causing you issues (that most times in that part are due to wrong 060 libs).
You can try the libs I used on my BPPC060 setup which I putted on my Dropbox for ya: http://dl.dropbox.com/u/939939/060_Libs.lha

To troubleshoot it, you can install a stock Workbench 3.1, then install the 060 libs, then install Piru's WhichAmiga and check if it see's normally your CPU etc.
Also check if everything's stable and then move on to 3.9.

johnim made an awesome guide @ Amibay and EAB about setting CWB3.9 from scratch, which you can check out here: http://www.amibay.com/showthread.php?t=20315