I first saw this problem at MD mod meet 6 where DBG pointed out at least one owner's roof worn through contact with the trunk liner. The problem occurs at the rear fold where the sides of the roof crease out and the points of the creases rub against the side walls of the trunk liner. If you raise and lower your roof enough times this wear issue
will happen to you!
Going to MMM7 last week reminded me that I was going to do something about it, hence this mod. Basically all it is is the addition of a drilled hole and a push pin on each side to cinch the carpet liner back tight against the trunk wall, away from the roof crease point. Takes maybe 10mins a side if you do it slow.
Even if you don't believe you will get this wear problem, I found that the mod (surprisingly) allows the roof to close down far more easily now, requiring little or no pushing down before closing the trunk.
OK, so this photo shows the wear point (passenger side) that I'm talking about...
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First put a strip of masking tape where the roof crease is, marking the point where it touches the liner. Then press against the liner with your finger and find a place about an inch back from the crease point where the carpet liner is most easily pushed back to the inner wall. Mark with an "X" (Note: I found this was not at exactly the same point on each side of the trunk due to differences in the liner shape.)
[attachment=2]
Now, using an awl or other sharp pointed instrument, make a hole in the carpet at the X and while pushing the carpet back against the wall, scribe a mark in the inner plastic with the point, where you'll need to drill.
[attachment=3]
Pull the liner out and away and
carefully drill a hole in the trunk wall.
DO NOT go too far or you might hit something behind.

You'll also need to enlarge the hole in the carpet.... I did mine by melting a larger hole with a propane-torch-heated philips screwdriver.
[attachment=4]
Now put the liner back in place, push against the wall, lining up the inner and outer holes, and insert your clip. You
could use a regular "christmas-tree" panel pin, but I preferred the expanding type with the screw-in center post. It's a firmer lock, and yet is easily removable if you need to get back in there or ever get the liner out.
[attachment=5]
Here's the pin in place, carpet cinched back:
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Rinse, repeat, for the other side...
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... and the end result, showing the clearance...
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EDIT: For people asking about clips/pins, this is what I used. Got mine from Pep Boys ($2), but seen them (or similar) at Advanced Auto and similar stores. These ones take a 1/4" drill bit for the holes...
[attachment=9]
Good luck!!