Toyota Repair: 2002 Toyota Tacoma Xtra Cab V6 Manual TRD wont start (54k Miles), passenger floorboards, plastic moldings

Question
My Tacoma has what I have heard is a "typical" body seam leak somewhere behind the dash in the cab. When it rains hard water will pool in the drivers and passenger floorboards. I have had it looked at by a glass shop here in town (recommended by the local dealer) and was told it was a common problem with the Xtra cabs and 4 door models, and that it could be resealed. They had it for a day or so and they had a hard time finding exactly where the leak was and told me to bring it back after the holidays when I could leave it for a longer period of time. I drove it home (with parts of the interior plastic moldings still on the floorboard) with the intention of taking it back as soon as I returned home from the holidays. I left it five days and my fiancé returned to town and she cranked the vehicle and moved it to the side of our driveway on a Monday. It rained pretty good that Thursday and Friday. I returned home that Saturday and went to drive the vehicle back to the shop and the battery was completely dead. I hooked up jumper cables and tried to jump it. Once the battery had enough power to turn the motor over it still would not start. Later that afternoon I went back out and tried again and the battery was dead again. I pushed the vehicle into my garage and unhooked the neg. battery terminal, recharged the battery and tried it again. It would crank but would not start. I realized that when it sat there was a draw on the battery, so I used a test light between the loose neg terminal and the neg post on the battery. I went through the fuse box underneath the hood pulling fuses until the test light went off. It went off when I pulled the 20 amp EFI fuse in the box right behind the battery. I can only assume that there is a problem with the EFI that is not allowing it to start and is draining the battery down while the ignition is off. Can you advise what I can do to narrow it down the problem further?

Answer
Toyota has issued a service bulletin addressing water leaks on this model tacoma, I can send a copy of this bulletin to you if I can have an email address. I also have seen a couple of cases where water leaked in on the right side where the computer is and getting into the computer and  destroying it, the leak is not caused by the windshield, resealing the windshield will not solve the problem, like you said it's a body seam leak, it's below the plastic cowling and can be verified by removing the plastic pieces and pouring water in to the area and looking inside with the glove compartment removed, you may see water dripping down directly on the computer.