Hi vsr123,
You have dropped a few names in your post but haven't explicitly said, for instance, what a Gainclone is ... so we may not be able to help you much. However:
A. You said " ... then went from the CD --> GK-1--> Aleph 3 and it sounds just fine, so I know that there is nothing wrong with the GK-1."
B. You also said "I initially thought of using the GK-1 as a volume control/pre-amp, but I am wondering if it is useable now?"
With A, above, you've just proved to yourself that you have a fine system: source --> source selection & vol control (ie. pre-amp) --> power amp --> speakers.
The GK-1 *IS* the pre-amp ... just as you surmised in B.
Regards,
Andy