Thought I would post an update:
Had time to play with the top/clam shell and as suggested by EJ-Fresno I checked the gears on the passenger side top transmission, which indeed have a few cracked gears.
All other components checked out fine, I was able to disconnect the transmission cable to motor on one side and by touching the top button to raise the top a little at a time and was able to get top clam shell aligned enough to lower after hooking back up the cable.
Now I was in need of a new passenger side top transmission, thought about buying a used one here on the board, but really I would just have the same issue later if I replaced and old one with another.
Went on Pelicanparts and each are selling for $704.00
Did a little more searching and found an eBay seller that makes the gears out of metal so you just end up replacing the broke plastic gear inside with a new metal one.
Cost for both passenger and drivers side gears with USA shipping: $199.00
If anyone is interested here is the URL:
2 New Porsche Boxster Convertible Top Transmission Gear Gears L and R Side | eBay
Once I install I will post a follow up.
