I'm booked JNB to JFK, leaving this Tuesday. There are Y to J upgrades available on the JNB to DXB leg (at a cost of 46800 miles) but not on the DXB to JFK leg (at a cost of 70200 miles). I have searched the flight and there are still Saver business class tickets available. I suspect that an airport upgrade is probably possible under these circumstances, but my understanding is that on arrival at JNB, I won't be able to upgrade both legs, and since the miles cost to upgrade the entire journey is 70200 (ie, ahead of time, they essentially give you the first-leg upgrade "for free" - weird!), I don't want to upgrade the two legs separately - I don't have enough miles for this anyway. So my best hope is that upgrades get released ahead of time, because if upgrades are available on both legs ahead of time, I think I can do a single upgrade on both legs for a total cost of 70200 miles. Hence my question: what are the chances of an upgrade becoming available on the DXB to JFK leg ahead of time? Thanks.

Unfortunately there is no reliable answer to your question. It all depends on the load at the time and the expected sales of seats. If the load is still low 2 days out, the probability of award seats being made available increases dramatically. I had a Quick Look at ExpertFlyer for Tuesday 26 May and all three flights that day have a lot of availability in all cabins and in all fare buckets. So that is promising (although a lot can happen in 5 days).
If you want to take the risk that upgrades will NOT be made available in advance of check in, you could grab the available upgrade on DXB/JFK now (it might disappear!) and keep on checking if there is upgrade / award availability for JNB/JFK. If so, phone the call centre nd ask them to upgrade you and to combine the two upgrades so you only �pay� the �through rate�. Do NOT upgrade that second segment using MMB (it appears you would not have sufficient miles anyway) and do NOT set auto upgrade (again, you would not have the miles for that to work).
Several people here know that upgrades come to those who work at it!
Good luck.

Thanks, thijsseh. To be honest, I'm not that interested in the upgrade for JNB-DXB - it's a shortish flight on a 777, so seems a bit of a waste of valuable miles if I can't get the onward upgrade. In the old days, the upgrade of the second leg would be quite a bit cheaper in miles than upgrading both sectors, but it seems that's changed and now upgrading only the DXB to JFK leg costs the same as upgrading both sectors - extremely irritating!
I do have an alert set for upgrade availability on the second leg (alert only, not auto-upgrade) - are these alerts reliable or should I keep checking manually?

I have found the alert sort of reliable, but I would also check manually and even phone in.
I had misread your original post. I assume you are booked on EK 203 to JFK. There too they are still selling J Saver seats (EF shows O7), so there is a chance.
If you are happy to spend the miles on just the DXB/JFK flight you can always try at DXB (Skywards desk at the escalator to the lounges in B concourse or in the lounge if you have access through silver or above status). Or even on board (ask the FA at the door when you board and someone will come to your seat). The miles for these options are the same as when doing it via MMB or the call centre.

I'm actually on EK201 to JFK on 29 May - I booked a long layover so I can get a hotel night's sleep if the upgrade doesn't come through.
Attempting a 9-person business class booking on that flight shows Saver available, so presumably business class is pretty empty at this stage.
I'll check at the Emirates lounge in Dubai before my flight if nothing comes through beforehand.

Upgrade came through!!! I've just checked on my booking and an upgrade was available for the whole trip. Yay!! So much for the auto notification - didn't got one!

Good result.
And well done, as I said earlier: upgrades come to those who put effort in it. Or something to that effect!

...and luck.