I don't have 3.9 (yet), so I use "ffstd64.lha" (on Aminet) to use >4Gb hard drives.
The easiest way to use it, is to take your 3.1 floppys (The Install disk) and switch FFS files (Can the one on the disk and add the FFSTD64) and set everything up as normal. I'm running a 20Gb drive in my A1200 this way with no trouble.
I did add OS 3.5, and this setup has worked fine for years.
If you have 3.9, it should be even easier.....
Good luck................
