I've never had any major issues with 3.9, but using SFS or PFS on the offending partition will solve your problem.
SFS (current versions) will not help without a replacement for scsi.device.
one partition does indeed cross the 4GB border
You could make that partition a bit smaller. Loosing 100MB shouldn't be such a big issue on a 4GB drive.
I am debating if I should just install OS 3.9
Just make an emergency boot disk and try it out before you change anything on the HDD.
iirc, the 'ROM update' file caused the machine to hang up, until I installed BB1 + 2. Any advice would be great..
You can always choose to boot without startup-sequence from the early startup menu and then rename the file.
Basically, in a worse-case scenario, I am not sure if I could boot from a floppy with access to my CD drive(s) so I could restore WB from my backup, if needed.
You can use the OS 3.9 emergency disk. Or you could make your own boot disk with CD drivers. In either case you can and should test it before you start to make changes to the HDD.
Bye,
Thomas