the system folder I put on the floppy was the system folder originally installed on the hard drive.
Then that suggests to me the disk formatting interleave is the problem. The SCSI disk drivers were very finicky in those days. There's plenty of utility software developed after the SE which is not compatible with the Plus. And 230 files is nothing. Try writing large files to and from the disk and you'll notice a difference on the Plus. Obviously there IS a difference since you cannot boot from it on the Plus.
The only exception would have to be with the SE, since I have to boot it first in 7.1, then restart the computer to have it boot in 6.0.4 on the SC20 (but that does not bother me).
I don't really understand that one. Why do you have to boot into 7.1 on the SE? Just boot off the external drive directly by selecting it in the startup disk control pane (Also something the Plus can't do). Alternately you could get either System Picker or System Switcher which allow you to hold down a specific key combo during startup and chose which drive to startup from. Apple+shift+option+delete was the way to bypass the internal drive in later systems but no sure if that was supported in 7.1.
