There is still a 128gb limit with scsi.device?
Having a big hard drive with original 3.1 roms is pure luck, some drives doesn't work at all and some does.
As said you need to have 4gb or smaller boot partitio and after you have installed a OS, you need to patch scsi.device and fastFileSystem or use another filesystem.
As far as I know this is only scsi.device for standard A1200 ide wich works with any size hard drives.
http://aminet.net/package/driver/media/SCSI4345p
I have selfmade 1mb kickstart rom with that scsi.device and all possible filesystems.
This 400gb hard drive didn't work at all with 3.1 kickastart
Boot partition must be no larger than 1.9GB unless you're running a physical custom Kickstart rom with an updated scsi.device. I don't know the specific exact capacity, but personally if you must have a large boot partition then 1GB should be much more than any Amiga could ever need and so I'd choose 1GB.
Years ago, my boot partition was 10MB in the 90's. Now days, I'd probably make it 256MB as it's a nice round number.

Even though you have a custom Kickstart rom, the danger is that you could be soft-kicking 2.0 or 3.0 which will not have the updated scsi.device, and you could find yourself trashing your boot partition if you write any data to it. My advice... Keep it at 1GB (or 1.9GB).