Here is how I do it
NOTE: On thing that will change things slightly is if all the panel are original to the car and the car has not seen major panel replacement on the back half. The reason is that with original panels and no repairs you can use the original holes and pressure shadows on the panels to help realign them to one another. With out this everything is a new fit taking longer since no panel can be installed without effecting or influencing another in this assembly
1- All the rear panels. First the riveted panels and the trap door so that all the gaps can be correctly aligned. Don't forget to compensate for the bumpers. You can use paint sticks broken down into 2" sections staked and taped in place where the bumpers will be located or old bumpers with the bases torn off. Which often happens when you removed them
Test fit the rear carpeted panel (if you have a fold down) at this time of look also. You'll want it out of the way but test, test, test fit as you go along.
Trap door adjust up, down and side to side at the hinge bases. I normally remove the striker from the trap door so it does not scar the rear carpeted section trim if its an early car. Also leave off the plate on the carpeted section also at this point.
2- Install your fold down retainer or non- fold down hardware to the wheel housing at this time
3- Quarter panel trim (rear seat side panels) and then the uppers
4- Fold down seat section next. Again checking fit of the rear carpeted section or non- fold down board before tightening down the section. Also check the fit of the fold down section to the quarter trim moving the section slowly and carefully as and clearance issues now can result in scratches in those panels. Make sure you used the correct screws when installing the trim around the fold down and carpeted sections. Large head screws will stick out an additional amount, reducing clearance and producing (at times) scratches on near by painted/plastic panels
If there is (clearance issues with the side quarter panels) , remove fold down or place it in the up right position if it can be safely and adjust the quarter trim, in, out, forward or rearward (if you can) The floor attachment points allow for at least 1" forward and rearward adjustment while the sheet metal can be flexed side to side at least 1/2"
- I then do the thin trim molding between the panels since I can now use the fold down panels as a base to work off of then the two over the head panels forward of the rear window. Of course you've installed the head liner and rear window long before you started the fold down install
- Would install the seat back and then the seat bottom after everything else is in place and adjusted.
- Make sure your seat belts are installed BEFORE the rear quarter trim panels are installed. Many of have had to retrace those steps
Hope this helps - just what has worked for me