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Ok. Not really focus stacking then (that's specifically stacking images for increased depth of field with a moving focus point). Stacking images for motion works pretty well at night like this, but the intervalometer is going to cause issues (like the stutters you see here, which you may like, but I personally think looks like an error, but that's me) because of the huge delay between exposures. Better (again, in my opinion) to pick up a nice thick ND filter to enable a minimum of 30 second exposures, then stack if you want longer (I have a 10 stop and 3 stop which allows for 2-5 minute exposures in daylight, which I've done and I prefer to stacking...for longer, I'd stack). The key is to have the vast majority of the image made up of actual exposure time. If you're shooting without NDs and stacking every two seconds, you're only capturing a very small fraction of the actual time and movement and you won't get good results.
Also, to avoid stacking delays at all (since the X-T1 requires a minimum of 1 second between exposures) pick up a remote release, set it to continuous shooting and lock the button down. I recommend the Vello RS-C1II remote...it's made ostensibly for Canon, but works with any camera that can use the mini sub (mic) port for a remote release, and the Fujis work great this way. It's flawless on my X-T1, and it costs a fraction of what the Fuji RR-90 costs. I reviewed it here: http://admiringlight.com/blog/mini-review-vello-rs-c1ii-remote-release-fuji-x-t1/