i can't see why do you want to use ffs on the boot partition... go install the latest
sfs for os3.x, i use it on both of my amigas on all partitions and it's rock.
check
greg donner's os3.9 faq for any fearther help.
p.s. 1 i hope that you boot from the emergency disk first and install os after...
p.s. 2 have you try yet to install the boing bags 1&2?
amiga os 3.9 updates