It's worth noting that the AWS EC2 99.99% SLA is a regional SLA, i.e. it only covers a situation where multiple AZs are down simultaneously.

One AZ going down is not covered by the 99.99% SLA. AFAIK there isn't any per-AZ SLA, only a single-instance SLA of 99.5%. The effective per-AZ SLA is going to be somewhere between the two.