Firstly, yes, they're all Amy & Frank - each is one of the simulated couples who climbed the wall.
The couple we are focussed on is simulation 998, which matches the number of rebellions logged...
We have to assume that this is couple 1000 & that the two simulations who did not rebel are somehow still inside the simulation. Their fate is not mentioned, afaik. Presumably once the final results are in, all the simulations are terminated & the occupants are never aware. We do see all the rebellious couples 'dissolving'.
As regards the math, or processing power needed to perform these simulations, you always need to be aware that Black Mirror never concerns itself with the science behind the technology. It simply asks you to believe that at this point in time, technology is sufficiently advanced to be able to achieve it.
How is rarely important to the plot.
The show is more usually concerned with the human implications of the technology - how we interact with it, what it makes us do to ourselves & each other as a result of it.
If we assume the app uses proximity of signed-up members to generate 'quick' matches, then either it tested everybody in the bar, very rapidly, or only Amy & Frank were signed up. It really isn't important which, merely that the results echoed the claim from the beginning of the simulation that the chances of eventually making the correct match are 98.8%
The final scene imho just gives some "aww" factor, when we see that in real life Amy & Frank are about to meet for the first time... & we, the audience, are pretty certain they will 'live happily ever after' - which in itself is quite rare for Black Mirror :)