So, Trans is making a god awful whine again, and the oil level is good, Could it be the Input shaft bearing as it only happens when the clutch is pressed.

sounds more like a release bearing. with the clutch depressed the input shaft is disengaged from the crank.... assuming the pilot bearing hasnt seized and locked your input shaft to the crank

I am not sure? As I was talking with a Tech from my work, he says Mazda's are different in how the clutch system works. That's why he said input shaft bearing. Is there any way to check?

the only way to be certain is to take the trans out and spin the clutch release bearing by hand, you should hear a noise from it it might sound like its dry or worn out. a new one wont make any noise at all. the clutch works the same on this car as any other..... i guess the tech just didnt want to mess with it... i cant say that i blame him honestly

the clutch is the same as any other car, dont know why he would think its different.

if the tech didnt want to mess with it, he's irresponsible

The Techs a good guy, I work with him. I don't know where he got that there was a difference in the way the transmissions are setup to work in mazdas, but he's saying that instead of pushing (or pulling) on the bearing it is pulling(or pushing) I can't remember.

Maybe it's different in Europe who knows?