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No need to disconnect battery when installing the waterproof case, at least they don't tell you to do that and I didn't when I installed mine. But aside from possibly having to enter your radio's unlock code and clearing of your emission test ready codes, I can't think of any reason not to.
Specialized ECU recommends that you test things before closing everything up, but I'd recommend that you hold off on testing until it's all back together because you could set an airbag/seat-belt code if you power up with the seat out. I have a Durametric cable, so I didn't worry about that (I just cleared the code).
They recommend that the big connectors be disconnected in a certain order, and I would do it in the order that they show in the video (and in the instructions that come with the box).
Lastly, I recommend that you make absolutely sure that the board is 100% bone dry before you seal it up in the waterproof case.
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2001 Boxster S - Speed Yellow, Black Leather, Tiptronic, Jake Raby rebuilt 3.2 with IMS Solution
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