Engine simulation would be considered as part of the AFM, I assume. As with the flight dynamics, the engine and fuel simulation would have to be written from scratch within the AFM. There are no tools available.

While it is true that the electrical system (AC) is dependent on the engine, so are several other systems. In reality, all you need is the data (RPM) out of the engine to make the AC electrical generator work. This wouldn't need to be incorporated in the same AFM dll.

There have been a lot of questions of what the new FC3 Advanced Flight Model (AFM) for missiles entails, so here is description of some of the new features:
Launcher platform speed, thrust, missile weight, total drag, gravity, etc. are all calculated to determine missile speed.
Missiles now incur realistic energy bleed that accounts for drag, induced drag and gravity. Induced drag calculates g-load and that factors the missile’s lift. Missiles will now bleed energy very quickly if the target performs hard maneuvers.
We added a longitudinal-load fuze arming type. The missile warhead of missile will only be armed after reaching the assigned longitudinal g-load (acceleration). Otherwise the missile will not detonate.
We added a limited duration to the missile’s power system (gas-generator, generator and hydraulic pump). When the onboard power system is exhausted, the missile goes ballistic.
We added a self-destruction timer. Some missiles will self-destruct when the timer is reached.
We added altitude based of self-destruction. Some missiles will destruct when reaching an assigned altitude above ground level.
We added a guidance timer delay. After launching a missile, the missile will fly straight from the from launcher for safety reasons before initiating the guidance stage. This is typically 0.3…1.5 seconds. For example: the R-27R missile flies unguided forward for 0.5 seconds before guidance to target starts.
We added parameters of loft trajectory. The initial range to target, the range of transition to proportional navigation, and initial angle of loft are all factored.