I have made a modification that stopped the squeak on my 08 clutch.
First the disclaimer. This will fix the squeak (noise) that stops when the clutch is slightly depressed. This will not cure a damaged TO bearing or transmission input tube, but I think it will prevent these failures from happening in the long run. If you do a lot of towing you might not want to do this because the fix reduces the clamp pressure of the clutch.
You need to get a mid 90's clutch MASTER cylinder from an F150. Inside you'll find a spring and collar. Remove and disassemble your slave cylinder and replace the spring with the F150 spring and collar. The collar fits on the peg of the piston that had the Toyota spring on it. It will be a bit of a struggle to reinstall the slave cylinder because the spring pre-loads the TO bearing.
The spring you need should be about 3" long, 5/8" ID with a rate of 5 to 7 lbs/in.
Many other vehicles (my experience with Porsche, Jaguar, Volvo and Ford) have pre-loaded TO bearings and I've never had squeak problems with their clutches. Bearings don't like to run lose and/or slipping.