First off... after drilling your holes in the trunk lid for your rack, "schmooie" a BUNCH of silicone sealant into (at an angle) the holes, between the layers of the trunk. This will help to distribute the load, giving support to the top layer of the lid and assist in averting the dreaded cracks. Then, those decorative metal washers that have a "Star" embossed onto their surface will further contribute in preserving the integrity of the lid.
Find a custom upholstery shop for the covering of your lid. Mine were done in '06 and are holding up beautifully. Mine were done by "Rocky" (member here). Not sure if he's back to this type of work though... he had a horrific wreck on his Valk and we almost lost him. I hear he's back to working, but has limits to what he's able to take on these days (but, getting stronger and doing "more gooder" than what was expected)... rock on Rocky !!!
Rocky decided my sand-blasted timing cover needed covering and made one for me.

Side view of the bags/trunk that Rocky covered in leather for me.

Some detail of his work.

This pic's a little grainy, same pattern material as the lower side of the bags.

Hind-sight? Well... one must be VERY careful with the "pointed DOG collar" studs. If I had it to do over again, I'd opt for the round "spots" that are more traditional. Rocky started this theme with the timing cover, and I had him just carry it over to the bags/trunk.