Boxster Immobilizer Module- under seat

[old911doc]

Sorry to read of your misfortune. I had the same experience with my '97 Box, except that the windows were fully up and the drain tubes all around were fully open. In really torrential rain, water enters the rear drain pans faster than the small tubes can drain it out, so the pans fill to overflow into the interior. Porsche engineers, in a fit of inspiration, located the water-vulnerable immobilizer right where the puddle would form.
I had a very good experience with Jorge at Specialized ECU Repair in Oakland Park, FL near Fort Lauderdale. He seemed to know his stuff quite well, and seemed a very straight-up guy, so I can recommend him for your repair. They have a good website, ecudoctors.com.
I would urge you get their waterproof box kit as well. It wasn't ready for sale when they repaired the immobilizer in my red Box, but as soon as it came out I ordered three for the three Boxsters in our family.
I would urge that this box should be fitted to all Boxsters at such time you acquire a Boxster. It's about one-fifth the cost of the ECU repair, and can be done electively in about an hour without any tool more specialized than a Torx bit, which is thoughtfully included in the kit. The car is ready for use immediately while the silicone sets.
And lastly, there is a really high-tech modification you should perform while you have the seat out; DRILL A HOLE ! A 3/8" hole under the immobilizer would likely avert many wet-immobilizer problems in the first place. I have drilled both left and right floor pans in all three of our cars and we haven't lost another immobilizer to water.