Jeff;
I am a complete noob at this, but I do know a couple of things that might help you until Ernie can chime in...my input added to your text in ALL CAPS:
#1 - I can enter in flight planning data into the Smiths FMC but the aircraft will NOT follow the flight plan in flight when the autopilot is activated.
-- It will not perform the plan when the GPS/NAV button is switched to GPS and the Autopilot is on with NAV selected. (and or with Altitude hold too). THE ISG GAUGE CONDUCTS LNAV BY CONTROLLING HEADING. IF YOU TURN THE AP ON AND HIT 'HEADING HOLD', WHEN YOU PRESS LNAV THE ISG SHOULD COMMAND THE HEADINGS NEEDED TO FOLLOW THE FLIGHT PLAN.
-- A: Do I need to remove the default FS GPS 500 gauge entry from the panel config file? (if one exists_)
NO. I USE THE DEFAULT GPS SOMETIMES, YOU CAN EVEN USE BOTH AT DIFFERENT POINTS OF THE FLIGHT. LIKE FOLLOW ISG LNAV TO THE TERMINAL AREA, THEN SET "NAV/LOC" HOLD TO FOLLOW A GPS APPROACH, ASSUMING YOU HAVE IT ACTIVATED IN THE GPS AND HAVE THE NAV/GPS SWITCH TO GPS.
-- B: Do I need to remove the NAV / GPS switch gauge entry from the panel config file?
AGAIN, NO...YOU CAN USE EITHER ISG LNAV OR GPS NAV MODE.
-- C: Do I need to modify or add to the autopilot settings in the aircraft config file or air file?
NOT AT ALL.
#2 - The breif ISG install guide references adding sections to the ISG Aircraft Config file. However, it does NOT specify if I must add the Aircrafts FOLDER name or its Title= name or Sim= name loacted in the aircraft's aircraft config file.
I assume the name to use is the Sim= name in the specifc aircraft config file. Is this example shown below correct and..
YOU CAN USE ANY NAME FOR THE ISG <AIRCRAFTID>.CFG! WHAT IS IMPORTANT IS THAT THE NAME OF THE CONFIG FILE BE CALLED OUT BY ONE OF THE ISG GAUGES (FIFTH PARAMETER). I HAVE CONFIGS NAMED B777, B747, ETC.
#3 - Do I just add all aircraft data to this one file (FS9/ISG/isg CFG) for all aircraft entries? Such as;
EACH AIRCRAFT SHOULD HAVE ITS OWN CONFIG IN THE ISG "AIRCRAFT" FOLDER.
Secondly does the "Add to" section shown above only go into the notepad GFG file located in the FS9/ISG/ folder?
EACH AIRCRAFT'S SECTION GOES INTO ITS OWN CONFIG FILE, NAMED FOR THAT AIRCRAFT AND CALLED OUT IN THE "FIFTH PARAMETER" OF ONE OF THE ISG GAUGES.
When I want to add in any other aircraft do I just add them directly below the first entries in this file or do I need to create a wholly separate config file for each separate aircraft? (I cound not find where this is explained anywhere in the default manuals) --- If so what specifcally must I name each file, what should it looks like, where is it placed, etc.
AGAIN, EACH OF THOSE ENTRIES GOES INTO ITS OWN <AIRCRAFTID>.CFG CONFIG FILE IN THE ISG>AIRCRAFT FOLDER. IN THE PLANE'S PANEL.CFG, MAKE SURE THE FIFTH PARAMETER OF ONE OF THE ISG GAUGES (AFTER THE X,Y,WIDTH,HEIGHT DIGITS) IS THE <AIRCRAFTID>.
#4 - I had updated the latest AIRAC files into the appropriate ISG/NavData folder but do they too also need to go elsewhere?
NEGATIVE.
My concern here is that the simulator itself must also have all the latitude and longitude data installed for all waypoints, fixes, VORs, etc in order to follow the advanced flight plan that the FMC creates. So...I am trying to distinguish between the .PLN vs .RTE files too. If so where can I get the navaids for FS or do I need to install the AIRAC files elsewhere too? Or...do I only need to purchase a flight planner like FSBuild to cure this issue? Again, the tutorials don't really explain how all this works. (AIRAC vs. Navaid data in the sim itself)
YOU LOAD THE ACTIVE FS9 FLIGHT PLAN BY SELECTING THE APPROPRIATE LSK BUTTON ON THE SMITHS FMS (LOAD ATC ROUTE)
#5 - Vertical Navigational Abilities (VNAV)
-- Is VNAV a sole function of the Smiths FMC or must I also have some other specific autopilot gauges installed in order for this to work?
SMITHS FMC. THE MCU ADDS SOME SIMPLIFIED FUNCTIONALITY AS I UNDERSTAND IT.
-- Is the VNAV ability a function I need to edit or install into the Aircraft config file or the aircrafts Air file? (can do if directed properly!)
NEGATIVE. IF YOU SET THE AP TO ALTITUDE HOLD AND HIT VNAV, IT WILL DO VNAV. SEARCH THE MANY THREADS IN THE FORUM ON HOW THIS WORKS...THERE ARE QUIRKS AND I DONT FULLY UNDERSTAND IT MYSELF.
-- If so what aircraft do you recommend that do have VNAV ability for file comparison.
SORRY NO HELP HERE.
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Good luck Jeff...I did a lot of reading in the forums to figure out what little I do know at this point

Matt