DarkEnergy,
That was fast! I'm really excited about where this might go; should be a great addition to the XR2. The ability to save multiple configurations is a GREAT idea.
As far as suggestions, let me offer a bunch of ideas. If I were doing this (which would imply that I know how to program, which I don't -- yet), I would say that if you're going to bother to write a configuration program, it should (ultimately) be comprehensive - i.e. completely replace the need to manually edit the config file. That said, I know that may take a lot of work, and even doing a subset of the things listed here would be really nice.
To that end, you might create a bunch of check-box style options that correspond to the on/off parameters in the config file - like whether the APU autostarts, whether damage is simulated, whether a "commander" rank is required to pilot the ship, etc. Ideally, hovering the mouse over a box would pop up a tooltip that contains Doug's explanation of the parameter (From the config file)
There are also a number of important parameters that take number or drop-down box input: things like main thrust, hover thrust, LOX consumption rate, etc. etc. These are all pretty important to tweaking the flight experience.
Probably least important are the audio callout enable/disable options. Those are easy enough to edit manually.
Personally, I find one of the last accessible/ most confusing areas of the config file is the custom Secondary / Tertiary HUD configuration stuff. Some kind of GUI for modifying those values would be AMAZING, but probably a lot of work.
Finally, you have Cheat Codes. I don't use these, but they would lend themselves easily to a check-box input.
Maybe you could arrange all of this in a program with multiple tabs - e.g. one tab for fuel and consumables, one for general ship behavior, one for cheat codes, etc.
As for how to handle failures in the scenarios, besides the Internal_Systems_Failure parameter, there are the following which set whether or not a specific piece of the XR2 is damaged:
DMG_0 1.000000 Left Wing
DMG_1 1.000000 Right Wing
DMG_2 1.000000 Left Aileron
DMG_3 1.000000 Right Aileron
DMG_4 1.000000 Landing Gear
DMG_5 1.000000 Nosecone
DMG_6 1.000000 Retro Doors
DMG_7 1.000000 Top Hatch
DMG_8 1.000000 Radiator
DMG_9 1.000000 Airbrake
DMG_10 1.000000 Left Main Engine
DMG_11 1.000000 Right Main Engine
DMG_12 1.000000 Left SCRAM Engine
DMG_13 1.000000 Right SCRAM Engine
DMG_14 1.000000 Fore Hover Engine
DMG_15 1.000000 Aft Hover Engine
DMG_16 1.000000 Left Retro Engine
DMG_17 1.000000 Right Retro Engine
DMG_18 1.000000 Forward Lower RCS
DMG_19 1.000000 Aft Upper RCS
DMG_20 1.000000 Forward Upper RCS
DMG_21 1.000000 Aft Lower RCS
DMG_22 1.000000 Forward Star. RCS
DMG_23 1.000000 Aft Port RCS
DMG_24 1.000000 Forward Port RCS
DMG_25 1.000000 Aft Star. RCS
DMG_26 1.000000 Outboard Upper Port RCS
DMG_27 1.000000 Outboard Lower Star. RCS
DMG_28 1.000000 Outboard Upper Star. RCS
DMG_29 1.000000 Outboard Lower Port RCS
DMG_30 1.000000 Aft RCS
DMG_31 1.000000 Forward RCS
DMG_32 1.000000 Bay Doors
IS_CRASHED 0
I think they're pretty self-explanatory. I'm not sure what IS_CRASHED means exactly (maybe that the craft is no longer pilotable).
Good luck!