I just did this 2 weeks ago and have been meaning to do a write-up but have been busy.
Just a quick word. The process I took was the least evasive as in I did not have to remove any panels. But the result is that there was limited space to work with. If you want more space then consider removing the panel in the 1st pic below. I tried to remove it but it would not budge and I did not want to break any clips.
Because of the limited space, you will want to pull down on the liner but doing so will stretch and crease it and thus it will not tuck back in like before you touched it. So try to refrain from pulling down on the liner more than you need to.
Please see 2nd pic below for the tools needed (racheting 10 mm wrench and panel/plug removal tool.) You can use a socket but again, there is not much room. And a flashlight will be handy and small hands and forearms.
1 – remove the 2 black plugs (pic below after removal) from the rear of the hatch using the panel/plug tool. DO NOT use a flat head screw driver as you will tear your liner. The plugs are pictured in the diagram above. The diagram above shows grab handles. This step will NOT apply to the RS. Once you remove them, the headliner is no longer attached so you can pull it down slightly. Look in the area where you removed the plugs and there are 2 foam pieces that are essentially spacers between the roof and the liner. When reinstalling the plugs don’t forget to incorporate these 2 foam spacers.
2- You will see 2 wiring harnesses (Yellow and Black). Unplug them. I had great difficulty unplugging them as there was a wire anchored to the roof right in the same area. I used my panel/plug removal tool and popped it out from the roof. Once you do this, this wire is out of the way and you can access the plugs much easier.
3- Using your 10 mm ratcheting wrench, feel your way and try to remove the 10 mm bolt. It is NOT possible to see the bolt unless you really pull down on the liner. Again, if you pull down on the liner you will stretch it and crease it.
4- once the 10mm bolt is free, the base is still attached to the roof due to a metal clip. Grab the antenna base and gently wiggle from side to side and up at the same time and the clip should fall off. Gently pull the base off the roof and you will see the 2 wires which you freed earlier. Reach back into the liner and locate the metal clip.
5- reinstalling the antenna base is the hardest part. Ford was clever in this design. The base can only go back one way. You can not put it back crooked. You will see what I am talking about it when you are doing this. Look below and notice the orientation of the base, metal clip and 10mm bolt. The clip has to be inserted from under the roof and can only fit one way in the base. This is what I did. Put the base on. Then from under the roof, insert the 10mm bolt through the clip and thread it in. As you tighten the bolt it will force the clip up and secure it to the base. Again, this will make sense when you are doing it.
6- plug in the yellow and black wiring harness and secure the 2 black plugs and you are done. Grab yourself a beer and thank me. BTW … I never drink beer during a project.