I initially started with a 32MB RTG frame buffer, it ran very slow. I then went back and set the RTG to 0 and only used the 2MB CHIP and 32MB Z3-Fast. It's running very smooth now. This is with kickstart 3.1 and WB 3.1 on a newly created 1GB HDF. I also installed Dopus 5.5 and Zak Mckraken to test it out. Zak seems to run very smoothely and the sound is right on. I do see some scanline artifcacts however, but they are outside the normal 800 x 600 screen size.
I'll mess around some more and see what happens.
EDIT: Well no go, seems the HD Toolbox can read the drive info but because it's so large it gives you back a minus amount on the HD size
Messing around with the Heads and Cylinders does help but will most likely fail as these larger HD's use the EXT13 BIOS options only available in the newer PC mobo's or separate controller cards like those from Promise and Adaptec.
Perhaps the latest 3.9 OS has an updated Toolbox to handle this?!?