Clamshell opens and closes, but top will not raise or lower.
 

I haven't found anything that discusses this with all of my Google searches. I have a 2003 Boxster S and up until now the top went up and down just fine. Today, I went through the lowering procedure and all that would happen is the clamshell would go up but the top would not move. I can manually lower the top and then push the button to close the clamshell. The same thing for raising it. I can push the button to open up the clamshell, lift the top back up and then push the button until the clamshell closes. I thought the clamshell and the top both worked off of one motor so I don't understand what is going on. Thanks for any suggestions the group may have!

On each side of the car, behind sits a "Top transmission". The top transition controls the movement of both the top and the camshell. In your case, the arms that attach your top to the transmission have become disconnected.

Put your top up and open the clamshell. Look at the rod that connects the clamshell to the transmission. You should see another similar rod that is attached to your top but is disconnected from the transmission. The plastic pivot is known to fail so see if your is busted or not.

Thanks for the tip! I'll check it out tomorrow.

Look at the third pic down in this link...

https://sites.google.com/site/mikefocke2/mikesporscheboxsterwebpages/clamshell-adjustment

Clamshell opens and closes, but top will not raise or lower.
 

Likely a broken plastic ball joint. Cheap and easy to replace, but don't buy a metal replacement. The plastic were designed to break in case something fouled the top opening or closing, and prevent serious damage. I recommend buying a spare or two to keep on hand.


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These 4 links are useful :
Porsche Boxster Convertible Top Transmission Gear Replacement - 986 / 987 (1997-08) - Pelican Parts DIY Maintenance Article
Porsche Boxster Convertible Top Repair - 986 / 987 (1997-08) - Pelican Parts Technical Article
Porsche Boxster Glass Window Convertible Top Installation - 986 / 987 (1997-08) - Pelican Parts Technical Article
They're not the same

Turns out I've got a couple of problems. First, yes one of the plastic ball joints was broken. However, the rod on the other side appears to have popped off and is bent. Here is a picture of the two rods:

http://986forum.com/forums/uploads02...1487692063.jpg

So it looks like I need one plastic ball joint and I either need to try to bend the rod back to the correct shape or get a new/used one. Any suggestions as to where to buy the plastic ball joint and the rod?

Next issue, cable on both sides are frayed. Where is the best place to buy new ones?

http://986forum.com/forums/uploads02...1487692179.jpg

Next issue, this hook holds down the top liner just behind the passenger side seat, but I can't find where it hooks. Any help?

http://986forum.com/forums/uploads02...1487692236.jpg

Finally, this cover piece was just laying in the well where the top goes down. Was on the right side. How does it fit. Should there also be one for the left side? If so it is missing.

http://986forum.com/forums/uploads02...1487692299.jpg
http://986forum.com/forums/uploads02...1487692317.jpg

Thanks for all of your help!