03' 5spd 4x4 Drivetrain issues

Sorry if this is a bit long, as I am new here as I just bout my first Tacoma last month.

Since buying, I have noticed a couple of issues.

The first being the clutch pedal does not always return all the way to the top. It gets almost all the way there except for the last inch, at which point it would engage the switch for the cruise control. I have been pulling it back with my foot for the last bit, when it hasn't returned on its own.

I am fortunate in the fact that I have every service record for the truck since it was purchased as the previous owner took the truck to the dealer for everything.

The Master cylinder and slave cylinders were replaced about 3 years ago. Just about a year ago, the master cylinder was replaced again.

Am I looking at a pedal spring issue or a master cylinder issue?

I have also noticed what I believe to be the sound of a throw out bearing going bad. When in neutral, I have some general mechanical noise from the transmission. When driving, mostly noticeable in 1st and 5th, I have a whine from the transmission.

Lastly, from about 63 to 75 mph, I have some shudder in the truck. I would attribute this to the center bearing on the driveshaft, but wasn't sure if it was at all related to the transmission as well.

Any insights are greatly appreciated.