Oooh boy....
It's so quiet around this board I feel obliged to say something... even though I never travel SA internationally in Y.
The SA website says that the upper deck has slightly more legroom (35" - which is a lot more than the 31" on the lower deck). Much more if you can snag the exit row - but beware the window seat in the exit row because the chute thingy in the door juts into the cabin. Like all 747's I've seen the upper deck has those neat "window boxes" for storage but they won't take a full sized carry-on. And the overhead stowages are also more cramped than on the lower deck.
As to general service levels: SA usually gets a fairly good rating (for a second tier carrier) on most surveys. Perhaps more than others a lot depends on the crew on the day. (Inconsistency is a bad thing, in general, but it does mean that you come across superbly warm and helpful crews from time to time. And it's a long time since I've had a truly surly one. A bit incompetent sometimes, but usually friendly and willing.)
In-flight entertainment features audio/video on demand and is quite good. Can't comment on the food in Y but the SA wines are usually very nice. ^
I've never heard of them offering cash upgrades to J. And since all the planes on this route now feature lie-flat seats there is a lot of demand and fewer seats. They don't even show award upgrades these days - it's waitlisting only - presumably so they can keep the J cabin full of passengers paying the full fare if possible.