Well I finally figured out what the problem with the speedometer/speed alert is which is stopping them from showing any speed at all, even though the speed sensor is working and putting out the km/h via a notebook through the ALDL cable.
First I checked the continuity of the cable with the multimeter and it was there and strong, so I swapped the ECU with the wives (we both have VS V6s) and it still wasn't working.
Today I figured I would have another crack at it and swapped my cluster over with the wives, to my shock it worked (so did the speed alert). OK problem is now the problem is isolated to the cluster, or so I thought. When I screwed it in it wouldn't work, but it worked when downwards not screwed in. I figured out that when it's in the upright position it won't work and the speed disappears but when it's downwards it'll work.
So as it turns out when I caused that short I actually did burn something out - Holden decided to use little "pins" made out of solder to create the connections in the cluster. I burnt out the pulse gnd "pin" (it probably disintegrated) which is at the bottom of the connection to the cluster (which uses ribbon style surface mounted connections to touch the "pins").
The solution to fix this most perplexing problem is going to be apply some new solder and hope my skills are good enough to not botch the job up completely (in which case the new solution will be replacing the whole connector). In the end I did need the new (old) cluster but I don't know about the speed sensor on the gearbox - at least I have a spare now ^_^. Fun times.