Just to clarify: when you say that you swapped in the ECU for the automatic, are you referring to the main ECU or the transmission controller (TCU)?
I'm not clear on what if any sampling the ECU would do of the TCU to determine gear position on the AW4 - my gut feeling is that for extended idle operation it would only check the state of the NSS as reported by the TCU and use that as a go/no-go condition to kick in the extended idle (or not, as the case may be). Where it makes sense to me for it to operate in this way is that it shouldn't care which gear it's in, just that it's in park or neutral, so sampling the actual lever position wouldn't seem necessary.
This has me wondering if what's really needed is an NSS simulator that can feed the ECU with a bogus signal. Of course, that's based on the assumption that the ECU firmware for a manual-transmission XJ has the capability to do that - and even if it has that capability, if it's active when a manual transmission (and hence no TCU) is installed.
It might be worth picking up a TCU and NSS and seeing what the options are for installing them in a manual-transmission model. My experience with manual-transmission XJs is very limited at best, so this may be way more work than the end result would be worth.
Late edit: I need to learn to type faster than Kastein