I could use some help!
If I recall correctly, hard drives generally aren't bootable under Kickstart 1.3. So your boot disk should have the startup-sequence file in it with the S: assigned to the directory containing it. Am I right?
If so, then the startup-sequence should assign all of the directories to the hard disk and transfer control over to it so that you can remove the boot disk from the floppy drive once booting is completed. Adding a few more assigns shouldn't hurt anything on the boot floppy then.