Okay, the *.mdl file is the model of the aircraft.  The is essentially the shape that shows up in the sim as the aircraft.  You cannot edit this without having the source files the model was created with.  These can only be gotten from the author.

The *.air file contains all the information about an aircraft, such as the wingspan, weight, size, engine and many other variables, most of which are overridden by the aircraft.cfg file.  You can edit this with several editors, available for free.  The most popular is AirEd, found here:

http://perso.wanadoo.fr/hsors/FS_Soft/fsairfile.html

The aircraft.cfg file is easier to edit than the *.air file, but it doesn't contain all the information the airfile does, such as the wing shape and others.  But it can be edited easier, and all you need is notepad.  Just open it and take a look.  Most of the sections are easy to understand, while others take some time and trial and error to get correct.

A WORD OF WARNING!
Don't change anything in the *.air files or the aircraft.cfg files unless you back them up first!  Just make a copy of them in the same folder by right-clicking on them and then clicking COPY.  Then click anywhere in the same window and right-click/PASTE.  This will ensure that anything you do to the files you can undo simply by replacing them with the copies.

If you have any more questions, feel free to ask here, or IM me.

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BOTH the *.air and aircraft.cfg file combine to control the flight dynamics of an airplane.

Most people that delve into flight dynamics start their editing with the *.air file and copy the relevant values to the aircraft.cfg file.

When you repaint, there is no need to mess with the airfile, only add another entry into the aircraft.cfg file.

Edit your textures to what you want them to be.  Then go into the aircraft.cfg and look at the very top.  There should be an entry labled [fltsim.0].  This is what defines each individual repaint as another aircraft.  To make one of your own, highlight that entry (everything down to the next set of brackets).  Now copy and then place your cursor directly below the last [fltsim.*] entry.  Skip a line and then paste.  You should now see an exact duplicate of the entry you just copied.

To alter it to make it your repaint, start at the top:

Change the [fltsim.0] to the next available number.  If the last fltsim entry is 3, yours should be [fltsim.4], and so on.

Change the title= to a different name.  This isn't important for the user interface (ui), but it tells the sim this is a different aircraft than the one above, and is used by the AI to input flightplans.

Here's the most important part: next to texture= put the name of the texture folder you have your repaint in.  For example, if the name of the folder is texture.repaint, the entry should read texture=repaint.

Just skip over the atc entries, they aren't important unless you have repainted in a specific airline.  But if you want to change them, go ahead.

Beneath those you should see three entries beginning with "ui".  These are the user interface entries that control where the aircraft shows up in your list.  The only one you need to change for a repaint is the ui_variation.  Name this whatever you want.

The rest of the entries are not used unless you have different panels, sounds or models for this aircraft, which it seems you don't.

Now just start up FS and see what you've got!

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It could be that you've left your repaint in 24-bit color which FS doesn't support.  At the very basic, you'll have to save as 8-bit color bitmap.  If you're using a converter to convert the original texture, use the same conveter to save it in the original format.

Also, DO NOT change the texture file names.