I remember what Wallace18 said they fit like, but then he got them to work.
What's the trick? At one point I smacked the engine cover and shouted "piece of #$%&!".
First Attempt:
I did it the measure way once piece at a time and secured each piece as I went.
I have a 9 foot long piece of precision ground stainless steel that was part of a linear bearing assembly that is incredibly straight and has a through hole every 3 inches. I found the centerline of 3 left/right frame members, dropped a screw through a hole and adjusted the rail until all three marks lined up with a screw. I measured other points of the frame to the rail and everything matched left to right. I now had a clearly defined centerline. I installed the side panels and secured with clecos and bolted on the rear bumper with screws and nuts. The crease in the top of the bumper lines up very well with the crease on the top of the rear fenders. The wheel wells line up very well too so I'm confident the rear bumper and side panels are where they belong relative to each other.
I found the center of the top of the bumper, lined it up with the rail, clamped the bottom to the rear of the frame, measured a few reference points to double check alignment, and put two cleco's in to hold it in place. I put the rear trunk cover on and it has a nice 3/16" gap between the rear fenders where it meets the bumper. At the middle of the fender the gap widens to over 3/4". Using quite a bit of force, I could push the fenders in and rotate them inwards as the flat flange that mates with the removable frame brace wasn't parallel with the ground. I could get one side close, but the other side wouldn't go close enough . Even with the best I could do, the body wasn't square. Moving it back to square messed up all the gaps.
Second attempt:
I said screw it, removed the clecos holding the bumper to the frame, placed the engine cover and trunk in place and just started shoving things around and duct taping them in place corner by corner without using the rail as a reference. This method actually ended up with better results than a more controlled measure and check approach. Go figure. Where the engine cover meets the side panels at the door jamb is super tight. Initially there was a 1"+ overhang but I could push the cover inwards until it locked with the side panel. The rear of the engine panel has a 1/2"+ gap with the fender. When I push the fender in, the trunk cover gets too tight at the back corner. I started shoving stacks of cardboard in between body panels to try and maintain gaps but only got so far as I still can't push the fenders in at the middle point where it attaches to the frame brace.
How big of a gap do you have where the engine cover meets the side panel at the door jamb?
How did you get the middle of the fender to push inwards and stay without breaking it?