Have you tried a CMOS reset--a tried and true fix for weirdness.....

The 4784 likely has an 8GB limit on the BIOS--are the other HDDs you've been
trying to use larger than that?

Unless you have some systemboard controller failure CS or master should make no
difference. And yes Setup should run from diskette no matter what the
condition of the HDD. That you can't run appropriate Setup programs hints that
a CMOS reset might help....

From older support files I see that:

(SP2141 ) Personal Computer Setup (Version 1.51C Rev. A)

(SP10245) Personal Computer Diagnostics

The first being what one would run from the FDD, and the second used for
installing the Compaq Diagnostic, I believe...

Dale