Yeah, the softtop fits both style doors. I love my half doors and haven't had any problems with leaking when it rains and they're fairly quit on the highway. My only concern is high crosswinds at highway speed. I could see the wind peeling back the top of the doors and letting the sun in just a bit. If it were raining, I'm not sure it wouldn't leak. The uppers are bulky when taking them off, but they're light enough for me to make two trips to bring them into my apartment including the rear quarter windows and the back window.
'09 X Unlimited, 4WD, auto, half-doors, soft-top
RC 2.5" Series II BB, JKS Quick Discos, JKS adjustable front track bar
15x8 Unique 297 (Soft 8), Goodyear MTR/Kevlar 35x12.50R15
5.13 gears, ARB front locker, Currie front shafts
Bushwacker flat flares, Rubicon rails with steps added