I assume that you are now talking about a 986? Regardless, the immobilizer/alarm module wiring is part of the main body harness.

No, you cannot bypass it.

Water damaged immobilizer/alarm modules can be repaired. BTDT quite a few times now. Worst case, it can be replaced.

PM if you need info.

The immobilizer, key fob transmitter (looks like a little pill), and ECU are all programmed as a set with a unique security code. If any one of those three components isn't working or communicating, the car won't start. If you replace any one of the three components, it has to be re-programmed to match the other two. Only a dealer or a shop with Porsche-specific diagnostic test equipment can do the re-programming (and they will likely check the VIN to make sure that the car isn't stolen). The enthusiast favorite, Durametric test cable, does not have this capability.

Used matched sets (immob, key fob, and ECU) can be found on eBay if you want to replace the entire set instead of having the immob repaired.

Remember, the whole point of the immobilizer is to keep the car from being stolen. If it could be simply bypassed, it wouldn't be a very effective security device.

You may have damaged an electrical component when you pulled the module without disconnecting the battery first. The connectors were a little tricky to get them back on so recheck to make sure they are seated properly and nothing bent. If you need the module tested, check with Qmulus as he fixed my module at a fraction of the cost to get a new one. See my previous thread.
http://986forum.com/forums/performance-technical-chat/64511-power-windows-not-working-after-wet-electronic-immobilzer.html