OK, will get the Update #3 and will let you know what happens.
In the meantime, moving on from the A340-300, I decided to give a go on configuring the Project Airbus A380-800. I looked at the FT KBOS AFCAD first and found gates that were labeled "Heavy" at terminal E had wingspans set from 30m to 36m. The aircraft config file of the 380 listed the wingspan at 216.7 feet which converted over to 67m. I chose a gate with what I thought was sufficient physical room to accomodate the 380. I then changed the selected gate in the AFCAD to 72m to be on the safe side.
When I executed GSX, I was given an error message, "The gate you selected is too small for GSX to operate" or something to that effect. Having set the wingspan to 72m, I was puzzled at the message. I decided to slowly slew the AC backwards in small increments from the AFCAD selected parking position and doing so finally eliminated the "too small" error message. So it seems as though GSX is also measuring the amount of space for any particular aircraft relative to the proximity of the physical terminal building.
What is really interesting here though, is when I called for "Deboarding", the airstair for L4 moved into position and extended to the bottom of the door sill, like it is supposed to!
I went back and re-tried the A340-300 and it still would not make it to the door sill of L4. I find it hard to imagine that L4 on a A340-300 is higher than L4 on a A380-800! I suspect as you mentioned that there may be differences in modelling, but L4 on a 340 being higher than L4 on a 380 just doesn't compute. Maybe it is. Common sense says it isn't!
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Update:
Installed revised Vehicle Update 3 and SUCCESS! Set the height to 5.55 and the airstairs extended to the proper height. Solved.
Thanks Umberto for your attention.