I don't see how a car clutch can work without a throwout bearing. I feel for you, facing such an expensive repair, and having doubt about what's needed. The place to look is the Chilton's Auto Repair manual, in the library. The Toyota folks should know what they're talking about. Throwout bearings aren't all that expensive, but if you don't need one, call it a discount. I have one suggestion though; While they have access to it, you should have the speedometer cable elbow ( that 90 degree receptacle) replaced. They aren't very durable and are a bear to get to when they do fail, unless you are already having the transmission worked on.
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