I have a 1998 GS400 and I have the same problem as the original poster. I can't find a way to deactivate the inmobilizer. The altenator is working. The battery is brand new. And all the fuses and relays are working ok.
I actually managed to start the car a couple of times (reight after I disconnected and reconnected the battery), but overall the car wont start.
Is there a key combination insert/remove combination or a pedal press/depress combination that may disable the inmobilizer?