I have YJ hard half doors with YJ uppers and they do not fit right with my 1/2 top. Drivers will not latch with upper on it.I run that set up now but with soft uppers. YJ half doors. TJ soft uppers. I had to cut the rear of the pins on each upper and reweld them (cutting the middle of the horizontal part). If you can find YJ uppers with the round upper corner, that would be easiest.
But if your hard uppers have the round corners, you should be fine. The upper round edge and the contour around the bump above the door handle kept me from using my two piece soft doors with the hard top.
I have YJ hard half doors with YJ uppers and they do not fit right with my 1/2 top. Drivers will not latch with upper on it.