I'm sorry to have forgotten about the CopyFromFloppy line. That's bit me in the backside so many times that there's a chunk missing there. I guess I must not miss that chunk all that much since I forgot about it.
The CopyFromFloppy will change from where the installer gets the BASEDEVs that get onto your boot partition. Without it, after the first part of the install, the system will not boot from HD. Luckily, there is an easy fix: Do the BootDisk/Disk1/Disk2 shuffle, hit F3 at the right screen to get to the OS/2 prompt, and use xcopy to get the correct .ADD files onto your HD. You should also be able to use TEDIT if you need to fix your CONFIG.SYS.
I hope the rest of the install goes smoothly.