QUESTION #1: As per the above, did you ever check that the 9V battery works properly?
I did not, because of the answer to question #3.
QUESTION #2: So when there is no lead acid main battery in the machine at all, that 9V battery would be keeping the 5.2V rail "powered all the time"?
Correct, the main 5.2v rail is required for PRAM value retention.
I do not recommend storing the Portable for any long-term period of time with a 9v battery installed. And thus have decided simply not to support the installation of 9v PRAM batteries. They often leak and cause system damage, similar to electrolytic capacitors leaking over time and corroding things away.
On the rest of your question, there's only one power input to the Portable internally. The battery harness carries power from both the primary lead acid battery and the PRAM backup battery to the system (9v battery has some series diodes to prevent back-charging). So using the discharge jumper would by necessity also drain the PRAM battery.
It is my belief that Apple never intended the Portable to sit unused for more than a month or two, which is my guess on how long a 9v backup battery would last.