the list of gates at JFK is very strange: I get high number gates with the label of GA parking and then some are RAMP CARGO.
This is not a problem, there's nothing to fix, and it has been discussed on the forum several times.
All parking positions in many of our sceneries are flagged as GA, in order to get rid of the default ground vehicles, which would otherwise conflict with the one that comes with the scenery and/or the static detail around the parking the comes with the scenery.
You can position the airplane much easier using GSX, instead of the default "Go To Airport" menu. After you start at the airport in any place (for example on the runway), call GSX, select a parking, and then choose the "Just Warp Me There" option. This will ONLY move the airplane, without activating the rest of the GSX so, you can effectively use it just as a better repositioning tool.
The advantage of using GSX to reposition is that, parking names are much better organized, grouped by Terminal with real world names, and you can also jump from parking to parking without triggering a reload.
The second issue is the missing terminals and lack detail in the taxiways and runways nothing is there.
Do you have both the "Addon Manager" and the "Couatl" menus visible under the FSX "Addons" menu ?