Are you familiar with Airport Design Editor (ADE)?
First, save a copy of the original AFCAD.
Next, open the FSDT KJFK AFCAD in ADE while JFK is loaded in the sim (you can keep both ADE and FSX/P3D windows open next to each other). Change your view in sim to top down (map view) and go to slew mode. Now, in ADE there is a button on the top right of the toolbar labelled "Connect." Click it. ADE will now be linked with your sim and a red circle with crosshairs will appear in ADE indicating your aircraft position. The location on the AFCAD will be same as your location in the sim. Now, slew to your parking spot of interest and position your aircraft until you are happy. Adjust the parking circle position, as necessary, so that it aligns with the red crosshair. If you double-click the parking circle a window will open that will allow you to change the type of parking, adjust the parking diameter, rename the gate number, and select what airlines can park there. Make your changes then save your AFCAD.
Cheers,
Todd