Ok - we've finally got somewhere with all this and our dealer.
As I've mentioned before, I previously chased our dealership twice about both updating the engine and trans programming - AND about the high pitched whine covered by Bulletin 03-03-16.
A few weeks ago we got S55 done (the trans loom check and update) - for which they did the latest engine/trans flash (we had no fault codes related to the loom so that doesn't need replacing at this stage - they just did the latest software flash) - and I asked AGAIN that they PLEASE address Bulletin 03-03-16.
After having S55 done we basically got a new car back!!
It drives like a normal automatic car now - period - and thank god!!! All the previous wierdness seems to be gone, with shifts nice and normal and predictable. There's a slight "pull" during downshift sometimes but I think that's the 4th gear (dog clutch) rev matching bizzo that happens under certain circumstances and is only noticeable under light braking.
At that time they FINALLY did assess the Bulletin 03-03-16 noise and agreed it was the applicable situation - so ordered the part. Our machine went in today to have Bulletin 03-03-16 carried out and we now have a high pitched noise free KL Cherokee - YAY!!