It's not very clear from your message if you have a "main pause" only, or several others.
JFK loading range is very small, smaller than what we usually do, because it's in close proximity with other large airports (LGA, EWR) and the dense Manhattan area so, since we control the loading of the scenery ourselves, we can prevent OOMs by loading JFK at the latest possible time. Even in P3D4, when OOMs are very unlikely, this will keep the fps reasonable.
So, what you call the "main pause", is the loading of the whole airport scenery, and it's normal.
If you have other pauses, be sure you have the anti pop-up slider in the Addon Manager at the highest level. If you already have it, then it's nothing that happens under our control, since when the "main pause" has passed, and with the anti pop-up slider at the highest level, we just load everything during that pause, and we don't load anything else after that so, any other pauses cannot possibly be caused by the airport, or GSX.
Also, SODE jetways in our airports are entirely static and SODE doesn't even know they exists, until the time you activate *one* of them, on ground.
I see you overclocked your system.
Your issue might simply be that, because of the extra load caused by the simple increased scenery complexity resulting from just adding a large airport with more detailed jetways, is causing higher temperatures in the system overall, so the Turbo-boost is going up/down, causing irregular fps spikes which you might see as "micro-stuttering" so, as counter-intuitive as it might seems, lowering your clock speed to the normal values might help, if you don't have a complex water-cooling system, (like the JFK's author has...) to keep the system cool.
And, if you have hyper-threading enabled, try to disable it in the BIOS, since many reports are telling P3D is way smoother with HT disabled.