I have exactly the same problem! Bought 3.9 a year ago and have been fighting shy of it since my ONE avbortive attempt to install it on my A1200.
I have 3.1 on there at present, plus a Blizzard 030/50 and the buffered IDE board with a 2.5" internal hard disk divided into four partitions, plus a CD Rom drive onthe other bit of the IDE interface, running CDFS.
I tried booting with a floppy and then installing 3.9 and it all went horibly wrong.
Is there any kind of resource out there that might help us?
Problem is that my original install has been so ulrta reliable I have forgotten all that cool OS install stuff I used to know!