What I would do is measure the mounting points, transfer that to the deck. Lay down some masking tape so not to scratch the decklid. The back of the wing sticks out 1/4". past the decklid. Put the wing on the masking tape, center the wing side to side then trace around the studs, then drill.
I...
The whole shifter will need to be replaced. It won't be long before you won't be able to get it in gear. Expensive item if you go to the dealer. Best place either a local salvage yard or ebay. Your also missing the trim piece that covers the gap around the shifter and the console.
I would imagine if you did a search on Ford Parts Giant with the different years and see what part numbers show up. Generally when something changes on a part, the part number changes.
Been a while since I did mine and Ford has you by the short hairs when it comes to hardware. I sort of remember buying special nuts for the brackets and the upper link.
I admire your efforts to get the windows working, but I think you maybe opening a can of worms. For one I don't think the window drop will work when you open the door or go back up when you close the door. I guess that's why it is called SJB. I would be looking to see if that SJB was changed and...