You really need to give us some more details on the system and os you're going to use. Every os and platform has is own limits and possibilities.
i.e. most 386 and 486 have a limit for 512Mb by default. Most pentiums go up to 8GB, but there you're into the PCI age with other solutions. XT ide bios extensions may overcome this limits.
DOS 3.2 Will go up to 30MB partitions, DOS 6.22 Will go up to 2GB partitions with the limit of 8GB hard disk and dos 7 wil give you fat32 with theoretically 128GB limit. You might look at Linux distro but I'm not into that too give you advice. Also look at software that can use space beyond bios limits.
Having a compact flash card is reliable and brings down stress on old hardware. And it makes it easy to transfer data from and to modern hardware. Newer harddisks (80GB + hard disks) will be more reliable and fill up the ISA bandwidth.
SCSI Will be an option, if you can find a controller and disks. Reliability is so-so because lots of these disks came from servers that were turned on for 24/7 on heavy load and thus are worn out.
So, where you at?