1) and 2) :
As Tom said, the *.air file contains most of the aircraft geometric and flight performance datas (as well as tons of hard coded informations like colours and autopilot systems) Unreadable unless you use a tool like AirEd (Air File Editor) By the way, you have to understand a massive amount of knowledge about aerodynamics and physics. Notably undocumented, the air file still has many obscure entries that only a few people knows about. The air file format is inherited from the early age of the Microsoft Simulator (maybe from the start, I'm unsure) The Aircraft.cfg (human readable) existed only, I think, since FS98 ? or FS5.x ? It was made to provide easy repaint variations installations and act as a modifyer for
some air file datas entries. It adds aswell new datas entries that, as far as I know, weren't available in the air file native coding. Once the Aircraft.cfg existed, an aircraft could not be recognized by Flightsim with this file missing.
3) :
Tom gave you a complete answer. Some details about the simulator engine side : how the aircraft behaves depend not only on the air file + Aircraft.cfg (the pair commonly, but somewhat incorrectly called
"FDE") but also on generated events/actions that can be triggered by :
- gauges (either hardcoded C/C++, which are basically Microsoft Windows Dynamic Link Libraries *.dll renamed to *.gau, or XML+BMP ones)
- modules (those dll like FSUipc, FSPassenger, AISmooth... including Remote control/Client based interfaces like SimConnect...)
- XML coded conditional actions, directly written in the 3D model file from a 3D modeling tool like GMax, 3DSMax or Blender (*.mdl - this way is limited to a few behaviour modyfiers though) XML codes in mdl are an extension concept of XML gauges directly in the 3D model.
(- user inputs - obviously)
As far as I can tell, only the gauges side is well documented. Modules and access to FS datas in memory is still very obscure at the time. XML codes in mdl are at "trial and errors" level.
Note that modules not only work for Gauges and aircraft. They have access to a far larger scope, like scenery or missions actions, graphics and sound injections, user interfaces, and may have access to FileSystem depending on their purpose and how they were coded (and many more because they are extensions applications/programs that interacts with the simulator) C/C++ Gauges have similar capabilities to modules, because they are relatively the same thing.
So, when you talk about "gauges logic", it involves cockpit instruments logic and aircraft behaviour, of course, but invokes the entire simulator engine that have input/output and interactions capabilities aswell. An "aircraft" with no visual model, but with specific gauges can become a local traffic terminal (ATC tower) to monitor and even control AI traffic flow...
4) : "A good tutorial" (ie a single one) won't ever exist I guess... because the topic is soooooooooooooooo wide you can't explain this or that in a few chapters. How to make a plane ? It's like how to make a screw, how to make a tire, how to make a nose, how to make an engine fan, how to make a seat (...) Those are basically 3D objects of different size and shapes that are all made of
points (vertices) and
polygons. So the question is not how to make a plane, but rather how to create objects in your favourite 3D tool... But planes has moving parts. How to make ailerons, spoilers, etc. It's not really how to make a plane, but rather what tools can I use to cut or merge parts in my favourite 3D editor and how to proceed... Learning curve of the tool itself. Then animations are also related to the tool. And aircraft are painted. 3D modeling tools usually don't have paint capabilities. They only apply existing textures (materials) and some have inbuilt renderers that just adds visual effects to the scene (shadow backing, reflections...) So creating a texture suitable for the model you're building is not really related to how you learn to make a 3D aircraft. It's rather graphical editor-side related.
...
And blah blah blah blah... It's boring because that's the way it is. There is NO shortcut. To be able to create a complete and working CaptainSim or PMDG aircraft, you'll have to do what others did :
1) Try
2) Re-read specific tutorials
3) Retry from scratch
4) Do researches on the web about a specific issue
5) Ask specific questions on forums - like here - if you didn't find any usefull info (did you searched that well ?) But heh ! No general questions like "how to build a plane"

You'll get either no further details, or an entire philosophic answer like this.
6) Try some arbitrary
weird things from time to time, just to have a look.. (Most useful techniques has been discovered that way; believe it ot not)
7) wander here and there spending hours reading what others have done even if at the moment, you don't really care about nor find that knowledge usefull at all.
8 ) repeat all the above while keeping good faith someday, you'll get this thingy shining in the sim...
^^ not only in 3D modeling, but in graphical skills (Photoshop/Gimp/Imagetool/etc.) at least some programming bits (XML language), file manipulator expertise (different compilers usage, regular file backups, simulator filesystem hierarchy, SDKs...)

Cook those continuously and you'll be no different from any other developper out there.