I think it's already been mentioned, but the noise on operating the clutch pedal is the clutch thrust/release bearing, often known as a CSC. (concentric slave cylinder)
It's very common for this bearing to growl or chatter as everything starts to get coated and caked in clutch dust.
It's no big deal, never had one fail and as the noise comes and goes when the wheels are NOT turning, it has nothing to do with wheel bearings or gearbox.
Your other, rotation related noise is more of an issue.
You've had the wheel bearings replaced and the brakes done and if they were done properly, you'd think that would rule those out.
But it's possible a "whooping" noise at speed could be a brake caliper binding.
You'd notice a hot wheel after a drive out if one were sticking on or it won't roll freely on a slight incline.
The noise can be quite misleading, I've just identified one on my lads C2 as it soundslike all four wheel bearings were grinding away and the inside of the car booms!
Another possibility is a worn drive shaft, there are two joints on each shaft, the outer joints tend to click and clack when worn, the inner joints tend to wobble about and whoop, quite often with a bit of vibration at speed, like a wheel out of balance.
They aren't easy to check, you would need to get under with the wheels on the ground and rattle them up and down to see if they flop about.
Another tell tale is jacking the car up and rotating the wheel back and forth while holding the inner joints casing, if the wheel/shaft rotate more than a few inches before the joint locks up (and starts rotating in the gearbox) then the joint is worn out.
Unless there's evidence of oil loss from the gearbox, I would not be tempted to jump to the conclusion it's a gearbox fault, especially if it selects gears ok.
Sure they can and have broken down, but there's usually a good cause that's easily spotted.
As you're out of warranty, I would try and take it to a gearbox specialist.
They will be very familar with driveline noises and what causes them.
