CWB OS3.9 is very nice, my default OS for the A4000 now as it has everything I need.
Installation works the other way round for CWB OS3.9, you need a clean OS3.9 with BB1&2 and then activate that with the CWB HDF.
After this you can add the other BB's but there are a few thing to move IIRC so maybe best to have a look in the EAB forums as there is a CWB section
Works great out of the box with just BB1&2 if you wanted to do a test run though.
Also when I setup my Amigasys4AGA on the A1200T I used the CD Drive in my Tower but I imagine it would also work on WinUAE, with CD Drive set up properly.
ADF's are very easy to find, look for the Amiga Tosec collection.
Steve.