Trade the Trektop for the oem Soft top?
Anyways, it's real simple.
Make sure it is connected to the brackets and the Door surrounds installed
Start with the top folded down
Bring the header to the connection at the windshield and leave everything loose. The rear pillars are folded inward on mine to be folded down easier
The front sunrider section will have hinges like the trektop does. Make sure it is not folded back like shown below
The front should be like this
The rear pillars will stay loose until the front header is connected to the windshield
Once the header is connected, install the rear pillars
The hardware should resemble this before you install the windows
After those are connected, connect the 2 side windows
Clip these into the door surrounds after the side windows are installed
Zip on the rear window (no picture)
That should be it! Hopefully that helped. I tried to make it as easy as possible. Once you get the soft top on there, it's straight forward. If you have any questions, just ask