Well, I was *going* to say that 2h+ was probably a safe bet at that time of day, but not *that* safe!
But your question now is delving into the realm of paid J passengers on standby for the flight vs. confirmed Y passengers on standby for an upgrade. Many gate agents prioritize the latter. I think if you confirm into Y, you'll have a good chance of staying at the top of the list as a paid J passenger (which I assume).
That said, there's currently 1 J seat left, if you are in paid J, you should be able to claim that, no? It's available in J/D/I inventories.
Alternatively, you could ask for a seat in row 17 which is normally crew rest on long flights and I believe has extra recline and a legrest. Not sure I'd want to get to SJU at 1:30am after flying in from Europe!