Just got done doing this on my Challenger. I'll help as much as I can. On the trunk drop off, the little flap goes on top of the trunk floor at least it did on my Challenger. The back section of the drop off (the flange portion that folds vertical up) should be fairly flush with the trunk floor flange. That and the floor flange form the shelf for the tail panel. They wrap up on the outside of the tail panel. Again this is how my Challenger is.
As for the rocker panel I hope for the sake of your sanity that you don't need to replace the whole rocker. Mine was only bad on the very bottom and half up the side back at the point where the quarter overlaps. After looking at the complexity of replacing the entire rocker I decided to replace just the bad section. I don't know if there are other areas of the car that have that many panels coming together, I hope not, but I did not want to open that can of worms. I cut off the lower section of the lock pillar to give me access to the inner brace that is spot welded to the rocker. In your first picture if you stick your head down by the rear wheel and look forward towards the lock pillar you should be able to see the flange on the inner brace I'm referring to. It is sandwiched between the outer visible portion of the lock pillar and the rocker. Once I had access to this flange I drilled out the spot weld and folded it up just enough to gain access to that vertical portion of the rocker. I then cut horizontally along that vertical portion forward until I was beyond the rust and then cut straight down to that lower flange where the floor and the inner rocker all meet. There is one problem with this method however, the profile of the AMD rocker did not match the profile of the original rocker very well and needed to be persuaded to the same shape. I have not got to the front of the car so I can't help you much on the front portion of the rocker. I'm hoping mine is good. I'm glad to see that you are replacing the entire outer wheel house completely. That was I think my biggest mistake. I tried to replace only the bad portions and quickly found out that Dodge made the outer wheel houses out of gum wrapper. The metal is somewhere around 21 gauge if there were such a gauge. The AMD outer is close to 18 gauge. Butt welding those two together was not an enjoyable event.
I hope I understood what you were needing and hope that my ramblings helped somehow. It looks like you have an original B5 Cuda there. My Challenger is also B5. Am looking forward to seeing a fresh layer of B5 on mine.
Oh, sorry I didn't take pictures and it is all buttoned up now. sorry for no visual aids.
