Top mechanism
 

Okay so the cover between the top and the rear decklid that comes up when you raise and lower the top. There is a rod that goes from a pivot towards the front. At the end of the rod is a red clip. It looks like the ball that clip goes on is broken or missing. Does anyone have an exploded view or some thoughts that can help me? I know i have not explained this well. I can try and post a pic later.

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Look through this tech article:
Porsche Boxster Convertible Top Repair - 986 / 987 (1997-08) - Pelican Parts Technical Article

If that doesn't help, show a pic of what you are looking at.

That helps somewhat. In figure 2 the red ball cup on mine is fine. The ball end that goes to is missing. It looks like it must have broken off because i could not find it anywhere. I need to figure out what size that ball is so I can purchase one. Thanks alot for the link, I keep forgetting how helpful Pelican parts can be.

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Look at this on eBay

New Porsche 987 Boxster (2009-2012) Convertible Top Push Rod Repair Kit

Push Rod Repair.
Couple of other options to replace the plastic ball ends with metal:
1. "URO PARTS 10 8693 010"
2. FOR PORSCHE 986 987 BOXSTER CONVERTIBLE TOP BALL PIN PUSH ROD REPAIR PART | eBay
3.Or the China source on Fleabay for the same/similar item - Search term " Stainless M8 Rod end" both ends are M8. These are use on some gas springs for hoods/trunks. Can substitute 8mm for M8 of course.
I found some as low as $4 for 2 ! How much did Porsche save by using plastic instead -really?