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Mike Focke's web page has great write ups regarding top R/R including getting the sides synced back up. I did two Boxsters last fall and found it to not be that tough a job (given that I studied the excellent write ups first!).
In general, I started with the top and the clamshell disonnected and aligned the transmissions individually by using a cordless drill attached to each cable. I then connected the rods for the clamshell and left the top rods disconnected. With cables connected to the top's motor, I lowered the clamshell to a few inches above the rear trunk lid and eyeballed it for level. If it needed adjustment, I simply disconected one cable and used the drill to adjust the offending side. It only took a couple of trys to get it right.
Once the clamshell is synced, your top will be synced. All you have to due is lower your top to a point where both pushrods can be attached.
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