Hi!
I've been doing some back reading and just noticed this post. (It probably wasn't visible at the time, as it was your first and needed moderator approval to show up)
About the aborts, many things are missing for that, namely ascent logic, but also a better OMS/RCS to allow for prop dumps during ascent. Better OMS/RCS will then need better logic to handle the orbit segment of the flight. So instead of making everything at once, I'm working first on the OMS/RCS and orbit for v2.0 (and it's already a massive rework) and then later I'll work the ascent, and aborts, as I'll have all that is needed for those.
As for the SSMEs failing, actually it is the SSME controller that shuts down an unhealthy engine. If you kill the power to the controller (yellow switches on panel R2), there is a sort of "dead-man switch" in the engine that will cause it to shutdown. The GPCs will have no idea what happened, except that the engine no longer sends data, and you need to press the correct Shutdown PB on panel C3 to let the GPCs know that the engine is gone. The failure handling in the SSME controller is more or less functional, but as there are no failures yet, it isn't exercised. You can always manually kill APUs, EIUs, MDMs and create an hydraulic lockup, command/data path failure, display and/or switch failure, and try to work around the situation... but there are no automated aborts yet.