I got a pair of qrtr skins from Year One that fit very good but that was a few years ago. Someone had a ragtop restore thread here with qrtr skins that didn't fit so good. Issues with wheel lip radius, etc.., so you asked a good question.
About the trunk pan... Someone here frenched in a piece from a Grand Fury , Crown Vic, or, I forget, but anyway the well large enough to fit a full size radial spare into. I thought that was a very smart mod .