My plan is to put the interior back together from back to front. The headliner is in, I have 90% of the interior stuff. Does the package tray go in before the sail panels and are the ends of the package tray turned up or down? Are the sail panels glued to the sides of the roof and metal strips towards the rear window?

The package tray should go in before the sail panels and the ends shoud be turned up so that they are behind the sail panels (when installed). If I remember correctly, I had to trim the ends of the package tray just a little.

The original sail panels were held in place by a couple of clips (like the door panels) and also by the headliner trim around the rear window and quarter glass. The sail panels usually have some extra material on them which wraps/glues around the metal strips you mention. One at the rear window, one at the quarter glass. Once glued in place, the headliner trim holds everything in place.

Most of the newer sail panels I've seen are sold with velcro patches that take the place of the clips. They dont really work all that great so I used a healthy amount of hot glue to stick the panels the panels in place.