Yes, I think that goes back to the same issue. I suspect you have to remove these items from the original before converting that file, then import the newly converted file into ADE to make your new terminal. You may then have to run your new obj file through MCX again to cement the new obj positioning, which I think is what you did to remove the old JFK jetway positioning.
The problem is that Ray converted every object in the airfield to a mdl (with position info), then incorporated that into the ad4 file - which also has position info for the default scenery objects it uses (which is every object!) so everything is kind of being called twice. Even the ground markings you circle are made up of default objects (GEN Traffic Line).
I have to say I think you're making an awful lot of work for yourself here. Especially as the basis for this airfield is Ray's parking arrangement which is now many years old, and will have been changed substantially in the intervening years. I think it would be easier to start from the stock airport (which includes all of the unique buildings), and make modifications similar to Ray's (but DO NOT convert the objects to mdls) but which reflect the current layout of the airfield. Alternatively, wait for MK Studios' P3Dv4/5 version of LIRF which includes the new terminals, which must be overdue for release now (and will be available in Orbx Central)! This is their MSFS version:
LIRF.