Well my work is now finished and it was easier than I initially envisaged.
I did try all 3 methods.
a - I found it too difficult to remove the 19 mm bolts securing the V levers to the transmission as they are loctited into position
b - I could not prise off the ball joints off the bottom of the black pushrod as I could not get a surface to lever off with the clamshell fully down
c - I found it relatively easy to remove the locking clip at the top of the black pushrod.
Here is my workflow for method c. I hope this will help others who get into the same position: i.e. unable to open roof when the clamshell is fully down one side.
1. Open the roof until the side of the clamshell that does rise is up about 100 mm (you will be able to hear the drive motor slowing down when it gets this far)
2. Unhook the black curtain at the rear of the parcel tray (there are two clips on either side – you should be able to easily see the one on the side that the clamshell is up)
3. Slide a portable fluoro light through at the back of the parcel shelf so you can see the inside of the side where the clamshell is still down
4. On the side that the clamshell is still fully down move the seat forward and remove the screen from the loop in the roll bar if you have one.
5. Reach through the loop in the roll bar and using a flat bladed screwdriver prise off the cadium plated locking clip that secures the top of the black pushrod to the bracket under the clamshell (refer to link to Tool Pants for images). Once I removed this clip the black pushrod popped off and the clamshell popped up. Hopefully you will be similarly lucky. If not you will need to push the pin at the top of the black pushrod out of the bracket. Now with the clamshell partially up on both sides you will have much better access.
6. Check that the grey plastic bearing sleeve in the clamshell bracket did not get damaged (mine did when the pushrod popped off)
7. Block the drain hole at the bottom of the side near the transmission (to prevent objects falling down and being trapped in the drain pipe)
8. Unclip the black plastic cover from the drive motor in the centre at the rear of the parcel shelf.
9. With a flat bladed screwdriver prise off the metal clip that holds the flexible drive cable into the motor in the centre.
10. Pull out the drive cable from the motor.
11. Disconnect the ball joint at the top of the black plastic coated cable that connects to the convertible roof near the V lever (you will be able to do this by hand - the V lever bolts onto the transmission and connects to the two pushrods). Laydown the cable to give better access in this area.
12. Remove the 19 mm bolt that secures the V lever to the transmission (this is Loctited in so will be tight to crack)
13. Move the V lever out of the way (whilst still connected to both pushrods) and remove the black plastic cover over the transmission
14. Remove the two black plastic nuts with large heads that hold down the rear of the black plastic coated foam drain cover which covers the transmission.
15. Rotate the black plastic clip attached to the pin at the base of the clamshell bracket (this secures the drain cover in this location)
16. Pull away the drain cover to expose the transmission
17. The transmission is held in place with 3 bolts. Check to see if there is an electrical connection going to the transmission near the bolt closest to the front (I had one on the passenger side of my 2000 Boxster S). If so plug out the cable plug.
18. Remove the 3 nuts securing the transmission (from memory these are 13 mm)
19. Jiggle the transmission off the 3 bolts and remove from the car complete with the flexible drive cable.
20. With a small flat bladed screwdriver lift up the black plastic tab that holds the flexible drive cable into the transmission and remove the cable (carefully as if you lift this too far the tab will break, as I only too well know –
21. Push in the new cable (later braided outer sheath part number is 986 561 171 03) into the transmission and clip the cable under the black plastic clips under the transmission so that the cable curves out (if you have broken the tab you can always wire tie the new cable back in where the cable goes under one of the black plastic clips on the transmission)
22. Jiggle the transmission back into position and refit the three holding nuts
23. If there was an electrical cable connecting to the transmission replace it.
24. Replace the foam drainage cover. Work along the top outer edge of the cover to make sure it is under the metal edge.
25. Rotate the black plastic clip attached to the pin at the base of the clamshell bracket (this secures the drain cover in this location)
26. Replace the two black plastic nuts with large heads that hold down the rear of the black plastic coated foam drain cover which covers the transmission.
27. Replace the black plastic transmission cover.
28. The drive shaft on the transmission is slotted to lock the V lever into the correct angle. At this stage the drive shaft will be in the fully down position. Rotate this drive shaft until slot is in roughly the correct position. From memory the slot should be about vertical. You can work out the correct position by checking the position of the V lever on the other side and rotate the drive shaft until the V lever will bolt into the same angular position. The drive shaft can be rotated by connecting a drill to the motor end of the inner drive shaft. You can use a variable speed electric drill but go slowly to make sure you are going in the right direction. I used a small manual drill to give more control.
29. Check that the V lever can be fastened back onto the drive shaft. Put some loctite onto the 19 mm bolt and refix the V lever.
30. If necessary replace the grey plastic bearing sleeve in the clamshell bracket (part number 999 924 130 40)
31. Lightly grease the pin at the top of the black pushrod and push the pin back into the sleeve in the clamshell bracket (you will need to lift up the clamshell slightly to get the pin in, if you cant lift up the clamshell far enough you will need to further rotate the drive shaft to get the pushrod in the correct position)
32. Replace the locking clip that secures the pin into the bracket (part number 999 166 075 02)
33. Unblock the drain hole at the bottom of the side
34. Reconnect the ball joint at the top of the black plastic coated cable that connects to the convertible roof near the V lever.
35. Reclip the black plastic cover from the drive motor in the centre at the rear of the parcel shelf
36. Measure the vertical gap between the clamshell and body at both sides. Rotate the drive cable until the gap is the same (within a few mm)
37. Push the other end of the drive cable back into the drive motor. If it will not easily go in rotate the inner shaft slightly (you will be able to do this by hand).
38. Replace the clip that secures the drive cable into the motor body.
39. Carefully raise the roof until the clamshell is nearly down on both sides. Check the gap between the clamshell and the body. If it is not equal you will need to close the roof until the clamshell is partially up, disconnect the drive cable and rotate manually again.
40. Once you are satisfied that he gap is equal try a full open and close operation.
41. If all is OK breath a sigh of relief and shout yourself to a job well done.
42. Note I recommend replacing the drive cable on the other side now as the likelihood is that it well also fail in the near future.