Aftermarket panel fitment

I know most aftermarket panels do not fit very well. My car at some point will need a new trunk floor, probably rear quarter repair, "from back of door to tail light area wrap around, not sure how high this will have to be cut. But probably trunk drop down pieces, and maybe even the pieces that tie into the upper tail light panel. Does anybody have any stories of the headaches they ran into doing this kind of work. I did find an NOS tail light panel so hopefully that fits well!!  And i probably need a new hood. Not sure if mine would be fixable?

i didnt do full quarters but some quarte patches around the wheel wheels front and back. That went pretty well. I also had to replace my trunk corners (Where the weather seal is) and the insert is a little different/tighter where the weather strip goes in but its still usable