Hi fastricky,
No, your annoying rattle would not likely be resolved in the process of replacing the convertible top cover.
Replacing the fabric top covering is, in my opinion, best done with the top frame left on the car with its mechanical drive parts left in place, as the top frame must be moved back and forth to different points in its travel as you work on different parts of the top. I have done three top replacements on 986’s and have never needed to have the frame off the car.
I have also done several gearbox overhauls, which require removal of the large ‘banana arms’ and the lightweight foam-plastic water drains to access them. If a gearbox were loose on one or more of the three mounting points, you might hear it rattle. Also, if the top frame itself was loose on its three mounting bolts, that might cause a rattle seeming to arise near the driver’s left shoulder, as you describe. An easy fix: the bolt heads aren’t difficult to feel, though they are difficult to see.
Other causes of rattling might include loose water drain plastic located underneath the front of the left rear plastic fender liner, the large aluminum diagonal brace ( attaches to chassis in front of the rear wheel), the front bushing of the long aluminum trailing arm of the rear suspension, or a loose rear undercar spray shield.
I suggest you check the tightness of the top frame retaining bolts first ( easiest to access), before going to the trouble of lifting the rear end of the car on stands and removing the left rear wheel. Make sure you chock the front tires both side before you lift the rear, as the parking brakes act only on the rear wheels ( but you already knew to do that.).
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