I just tested this version...is a version done by Toni- winuae author
it doesn't support big partitions without a new scsi.device
seems is hack or patch based on the PFS3 common version but no based on the direct scsi version
All-In-One means that both versions (PFS3 and PFS3ds) are merged into one version. Also yesterday Toni release a Romable version of his PFS3 handler.
You don't need an EPROM burner if you can make the ROM with Remus and then ask the IC company that provides you with the 27C800 to burn the image into the ROM before sending (They's only ask if you want it burned ByteSwapped or not).
Also... imho, the most valuable modules for making a custom ROM are:
- Icon.library
- SCSI.device
- Workbench.library
Trackdisk.device can be easily replaced just by an AntiClick program that requires no reboot

Also I can't understand how your HD works just fine without a patched scsi.device.
Scsi.device of Kick 3.1 is 40.5 alas your 39 version must be Kick 3.0.
Without a patched scsi.device you shouldn't have had more than 7.8GB as Thomas said whatever FS you'd be using.
As a referece, I'm pasting some info based on Thomas that I found in the past in Bloodwych's post for ClassicWB Big Hard Drive support:
Large drive support (>4GB) under Workbench 2.0/2.1/3.0/3.1 requires some limitations to be overcome in order to work successfully.
The two main problems are the hard drive controller, the “scsi.device”, and the actual native Fast File System (FFS). Both must use the same method to overcome the 4GB barrier; essentially you have to be sure the drive controller and the file system speak the same language or command set.
The three common command sets used in this tutorial are “NSD”, “TD64” and “Direct-SCSI/HD_SCSICMD”. If the hard drive controller and file system both support one or more of these, the 4GB barrier can be breached.
Here is a list of common controllers and file systems (Thomas et. al. 2009):
scsi.device V37/40: NSD -> no, TD64 -> no, SCSI -> yes, but only up to 7.8 GB.
scsi.device V43+: NSD -> yes, TD64 -> no, SCSI -> yes
scsi.device V116+ (IDEfix): NSD -> yes, TD64 -> yes, SCSI -> yes
cybppc.device (and most other Phase5 controllers): NSD -> no, TD64 -> yes, SCSI -> yes
FFS V40 and below: NSD -> no, TD64 -> no, SCSI -> no
FFS V43: NSD -> yes, TD64 -> no, SCSI -> no
FFS V44 (FFSTD64): NSD -> no, TD64 -> yes, SCSI -> yes
FFS V45 (OS 3.5 or 3.9): like V43
PFS: NSD -> no, TD64 -> yes, SCSI -> no
PFSds: NSD -> no, TD64 -> no, SCSI -> yes
SFS V1.84: NSD -> yes, TD64 -> yes, SCSI -> yes
SFS V1.279: NSD -> yes, TD64 -> yes, SCSI -> no
OS 3.5/3.9 overcome this limitation by replacing the “scsi.device” at boot and using a newer version of the Fast File System. The ClassicWB OS35/9 therefore has this support built in.
Other issues can arise from software such as defraggers and disk repair tools (eg Reorg and DiskSalv) not being able to work with partitions above 4GB due to lacking the necessary 64bit support.
This guide is for getting the original ClassicWB packs (and therefore Workbench 2.0/2.1/3.0/3.1) working with partitions beyond 4GB by essentially adding the support OS 3.5/3.9 already has.