I've got a 030 with 32Mb of RAM, so I'm set in that regard. As for why this has been problematic, I don't know. I've set up a 8Gb CF card before with PFS and had no issues. The HDTool (on the real Amiga) saw the drive just fine, and I was able to select PFS (custom FFS) from the men with ease, though it looks like with this drive I'm setting my partitions to high.
Anyhow, the reason I am trying a real hard drive and one so large at that, is because A. with a CF or SD card, Workbench always ends up telling me one of my partitions is corrupt, even after a fresh format and install. I always end up having to back up that partition, re-format, then I'm fine. Secondly, the 40Gb hard drive is as small as I could get my hands on for free.
I'll play around, see if I can get it, if not I guess I'll dance with the devil again, aka the CF and SD cards, though it really would be nice to use that 40Gb cause I want to install Half Life 2 on my hard drive. 
Use PFS3 AIO from aminet:
http://m68k.aminet.net/package/disk/misc/pfs3aioIf you haven't done so already, download the main PFS3 archive too:
http://m68k.aminet.net/package/disk/misc/PFS3_53Two more files are required: a replacement (updated) scsi.device and the LoadModule command. For the easiest I just got them from the ClassicWB_GAAE distribution available here:
http://classicwb.abime.net/classicweb/68k.htmLoadModule is available seperately here:
http://aminet.net/package/util/boot/LoadModuleThat's it....that's all you'll be needing most likely. I'm going to assume that your real Amiga hard drive partitions are to be labelled DH0: for your boot drive (Workbench) and DH1: for your Work drive (Work). Make sure your WinUAE partitions aren't labelled the same or you'll end up formatting them by mistake and that would be unfortunate. I won't be held liable for any data loss! Users are to follow this guide at their own risk!
From the pfs3 main archive, locate the pfsformat command and use this to format pfs partitions (copy it to your C: drawer on your WinUAE Workbench). That's the only file you'll be needing from the main archive.
Now, inside the PFS3AIO archive is a single file called pfs3_aio-handler. Copy this to L: on your WinUAE Workbench.
I personally use the OS3.9 HDToolBox but others should be okay as well. I'd start a fresh with the drive and get HDToolBox to detect the parameters (reset the drive). Sometimes this has to be done again if you find that it isn't saving partition or filesystem changes. Once it's done this it may ask for a reboot. But anyway, for a large drive such as 40GB I'd setup a boot partition of 1GB or less for DH0 (I use 256MB for OS2/3) and the rest can be your Work partition (DH1).
You'll need to remove the fast file system from the RDB if present and upload the pfs3_aio-handler in its place (located in L: now). This can be done under advanced options in HDToolBox or Change File System (I'm going from memory here). Check that both partitions are using pfs3-aio-handler and not FFS....and double check FFS is removed on both partitions. I can help you further with this if you're not sure. I also recommend 70-100 buffers for DH0 and 300 buffers for DH1. The Filesystem Identifier should be set to PFS/03 (0x50465303). MaxTransfer should be 0x1fe00, and Mask should be 0xfffffffc. I think HDToolBox of OS3.9 makes it look like 0x001fe00 or something....again I can check this if you need further help. All settings you enter in HDToolBox must be followed by the return key, or it may not register the changes. Don't forget to tick the box to make DH0 partition bootable. After you have saved the settings, HDToolBox should ask you to reboot.
After the reboot, enter this at the shell:
pfsformat drive dh0: name "Workbench" quick noicons fnsize=107then this:
pfsformat drive dh1: name "Work" quick noicons fnsize=107Both partitions should then be available. To verify that they are using PFS, type in this at the shell:
version dh0:Then repeat for DH1. Both should display a name and version number of the filesystem in use; this should reveal PFS and not FFS as filesystems.
So that's your partitions ready. You then need to install your OS to DH0.
Once this is done you need to get your hands on the LoadModule command and an updated scsi.device. Both of these are easily available and ready to use in the ClassicWB distributions. Under ClassicWB, in the SYS:MyFiles/LargeHD there are some further drawers. One is 128GB support. Find the SCSI_v43_24/Patched/A600IDE.scsi.device file and copy it to your Devs drawer on your new Workbench partition. And whilst your'e at it, locate the LoadModule command (in the Tools drawer under LargeHD) and copy it to your C: drawer on your new Workbench partition.
Then edit the Startup-sequence on your new Workbench partition:
Enter this at the shell:
ed dh0:s/startup-sequenceEnter the following line before any other command (this has to be the very first command to be loaded).
C:LoadModule SYS: Devs/A600IDE.scsi.device(I have put a space in after SYS: because if I don't I get a
smiley)
Save the changes and then reload the Startup-sequence to make sure ED hasn't trashed the top line (happens frequently to me, so I always make the top line a ";".
So that's it... Install the drive in your real Amiga and power on!
This above "rough guide" works for me, even with Kickstart 2 (37.300) and a 68000 CPU. That's how I'm using mine at the moment and I haven't had any problems at all. It will even work on machines without FastRAM. The scsi.device I chose here is the official one as released by Amiga International. There are more recent ones, but I've had no reason to use them yet, and I'm not sure under what circumstances they need to be used (I'm sure someone here will correct me).
There's a few minor details missing as I'm not by my Amiga or WinUAE setup, but I'll help in any way I can if you're still stuck.
If you're installing ClassicWB to your real Amiga drive, then the A600IDE.scsi.device needs to be renamed to scsi.device, as the LoadModule command is already present in the ClassicWB Startup-sequence and assumes a file name of "scsi.device".
