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