Good news on the upgrade side of things - my two upgrades that charged at the discount economy rate have now been adjusted and the extra points credited back. Just took a bit longer than the flight adjustments, but it is happening "automatically".
Another data point: me too!
I had six flexi-saver (V class) economy fares booked in February, before the cutover date. After the cutover date I requested upgrades on all six of them. Two are 'requested', but four were confirmed immediately, and points taken out at the discount economy upgrade rate. I contemplated emailing, calling, or talking to the lounge angels to try to get them fixed, but wasn't too worried as the flights are all still weeks in the future. I'm glad I waited now, as after 12 or 13 days all four confirmed upgrades have had the correct amount of points refunded to take the total to what it should have been for a V-class upgrade in the first place.
I plan to just wait and see with the SCs as well, but given my outcome so far and comments in this thread, I suspect they will happen automatically after a moderate delay as well.
Fingers crossed my other two requests come through!
mrpooky.