I tried that "mod" and now I get a blank screen(well I did delete the logo) and my hard disk light stays on forever. This is NOT an upgrade I had MS-DOS 6 and Windows 3.1 on the Fat(I think it's Fat and NOT Fat32) drive before.(and FreeDos before that). This is a sort of eraish-appropriate laptop(IMB Thinkpad 380Z).
UPADTE#3: Turns out that "mod" is for version 4 and I have version 3, so that's no good.
That technique also works in W3 and in v2.1 for that matter, I replace boot disk drivers all the time, the reason I asked is that as shipped W3 only sees hard drives of a certain size, simply because it was originally shipped in 1994 and HD's did not go above a certain size back then. The most common disk related problem when installing old versions of OS/2 onto hardware more modern that the OS itself (even computers from 1996/7/8) is that the drivers refuse to operate the hard drive because the BIOS is reporting size numbers back to the OS that the driver/OS thinks are impossible.
To fix this you need to 1) modify the drivers on the boot diskette and 2) Instruct the installer to copy the drivers from the boot diskette over the drivers the installer copied from the CD or floppy onto the hard drive because the drivers contained on the CD/Floppy install image are the same as the original, so will have the same error. This can also be done by hand by booting the modified floppy again after install and going into the command line and manually copying the files onto the drive.
This is explained in some detail in the original link.
IBM used to supply replacement driver install diskettes with fixes from FP40, but that site has sadly been taken down, but they do have a replacement driver set at:
ftp://service.boulder.ibm.com/ps/products/os2/fixes/v3.0warp/english-us/warpinst/ but it should be noted that this is outdated and the original method is recommended.