UPDATE FRIDAY 08 JUN 2012:
Put a call in with David this morning at 10 am and he indicated it was all connected to the line pressure monitoring kit and they were doing the finishing touches on the valve body tune. Could not guarantee with confidence that it would be ready and asked if I could call back at 2pm.

Thought, well, we have come this far, best hold it together and give him the room to tune to my brief.
Called back at 2pm and he was a little pensive indicating he was having trouble getting full alignment to my brief but that in Sports mode, all shifts were good but shift points could not be pared back to 6000 rpm. He was still working some more tuning and requested a call back at 4pm.... my heart was starting to get that sinking feeling, but I agreed heartily while swallowing my feeling of disappointment.
When I got off the phone, I thought I would be in a better position to turn up at the workshop at 4pm to get a closer appreciation of the issues and to see and feel the results for myself.
Got there at 4pm and no car in sight...

I suppose, real tuning does need a drive out on the road, so waited 5 minutes and David turned up in the car with a technician in the passenger seat monitoring the the transmission and engine through the OBDII port.
Prognosis is that the transmission itself is strong and they swear and standby the quality of the rebuild. They could not hard tune to my brief and they both indicated in separate discussions that there seems to be an interplay between the ECU and TCU in the auto which they have seen in other modern vehicles. Several parameters of the ECU are potentially used by TCU in managing the shift points and timing. Both indicated that MAP and/or MAF along with Requested Torque and Engine RPM are all potentially used by the TCU to manage the shift points. This makes sense to me.
So went for a drive in Sport Mode and it immediately felt much better in terms of transferring torque to the wheels (4 wheel spin in the wet) and the shift points felt stronger and happened at 6800 rpm on WOT. It behaved very similar to the when I first had the SC Kit installed, but now without bouncing off the rev limiter for a half second or more. So I am happier that it is no longer bouncing a couple of times off the rev limiter before changing. That was a definite concern and happy with this aspect.
In normal auto mode, the shift points occur too early like the line pressure is too high. But then if MAP / MAF are used by the TCU in determining the shift points, that would make sense as my car now has boost that probably means the MAP/MAF values are higher than expected by the TCU of an NA auto.
So after about an hour discussion and a couple of laps monitoring actual values (using my ECUdatascan), the technician (John) and David both concluded that the SC Kit has impacted the NA ECU and TCU interaction that results in the changed shift behaviour. It is not a cop out on there part. I confirmed the auto behavior they were observing was a direct result of the SC Kit install that I observed within minutes of collecting the car from HPF last year after the install. So nothing that David and John could do other than if I was not happy, they were going to continue to try to resolve with more time needed.
They had experienced this type of interplay between ECU and TCU previously with a boosted Commodore V8 (previously an NA) and they went through the drama 3 times back and forth with HPF but could not fault the transmission. So there experience with my car also brought back the recollection of the interplay between ECU and TCU in auto vehicles.
Discussed my options, including the changing of the ECU maps pertaining to Requested Torque and Throttle Angle and they suggested (without my prompting) to go to Springy Motors and discuss with a guy called Dan to see what he could do. I did smile and indicated that it was the next step in my build, so........
Yes, yes, yes....

Got my car back. Drove home and the stupid grin on my face is even wider now. The drive feels much stronger. Changes are happening consistently at 6800 rpm and it all feels strong. I was reduced to a giggling child most of the way home. How I have missed this car!
So, next steps will be off to Springy Motors to see what they can do in terms of shift behavior given the impacts of SC Kit on some of the parameters used by the TCU. Probably get them to do their engine tune as well (from scratch as I think HPF have locked their tune).
Full details of the precise build sequence is being compiled by David and sent to me in email. I will then post that up for those who want to devour it.
I did ask what torque rating they think the transmission has now and both David and John indicated that the additional frictions and steels in each clutch pack alone would double the torque rating compared to OEM (that would be around (350Nm x 2 = 700Nm), and then add another 20% for the improvement in the line pressures, so up around 800Nm rating is their estimate. Centre Diff was also rebuilt with additional line pressure and frictions and steels and they conservatively indicated it would easily be rated at close to the same.
And the costs you ask? Well, originally quoted $2800 for the transmission rebuild, then added $1000 for the Centre Diff, so $3800 all up. I knew this figure before I started and am happy that the price did not move in the end.