Your first argument seems to say that if someone simulated universe A a thousand times and then simulated universe B once, and you knew only that you were in one of those simulations, then you'd expect to be in universe A.

That's right, Nisan (all else being equal, such as A and B having the same # of observers).

I don't see why your prior should assign equal probabilities to all instances of simulation rather than assigning equal probabilities to all computationally distinct simulations.

In the latter case, at least in a large enough universe (or quantum MWI, or the Everything), the prior probability of being a Boltzmann brain (not product of Darwinian evolution) would be nearly 1, since most distinct brain types are. We are not BBs (perhaps not prior info, but certainly info we have) so we must reject that method.

What if you run a simulation of universe A on a computer whose memory is mirrored a thousand times on back-up hard disks? ... Does this count as a thousand copies of you?

No. That is not a case of independent implementations, so it just has the measure of a single A.

As for wavefunction amplitudes, I don't see why that should have anything to do with the number of instantiations of a simulation.

A similar argument applies - more amplitude means more measure, or we would probably be BB's. Also, in the Turing machine version of the Tegmarkian everything, that could only be explained by more copies.

For an argument that even in the regular MWI, more amplitude means more implementations (copies), as well as discussion of what exactly counts as an implementation of a computation, see my paper

MCI of QM