ok a little idiots guide for installing 3.9 on your CF via WINUAE (I'm sure there are better ones).
This is what I did with my 1200 setup.
1) Get a bigger CF (4GB SanDisks are nice).
2) Stick the CF in your PC's reader and perform a slow format under XP.
3) If you want to use SFS instead of the default FFS you can follow this handy
guide4) Start winuae hd with the saftey check disabled (eg winuae disableharddrivesafetycheck).
5) Setup a WINUAE config that matches your real miggy (rip your ROM from your real Miggy and use it under WINUAE).
6) Insert the OS 3.9 startup disk in your virtual floppy drive. Choose your CF as the one and only HD. Disable the 'add CDROM drive' option (the CDROM drivers on the startup disk should be enough to get your PC's CDROM driver mounted under WINUAE).
7) That's it, start WINUAE and you should boot to a 3.9 desktop with your 3.9 install CDROM mounted for you ready to be installed on your CF.
Alternatively you could just install AmigaSYS AGA and then bang in your OS 3.9 CDROM which will automatically upgrade it.
:-)