The adjustment for in and out is the post that the door latches onto. It takes like a 45 or 50 torx bit. And lube the latch jaws up good with a quality graphite dust spray. It might not be going all the way in to the second click. Which is allowing it to rattle.
When I put new weather strip on mine, I had to adjust that post out toward the body, cause of the new rubber.
'87 YJ, 4.2L built and bored, 8.5" of lift, 8.8 rear, AX15/NP 231, Tom Woods drive shafts, Flat fenders, 12,000LB winch, Custom bumpers, Rattle can paint job. Never completed...