Input shaft bearing?

I took my car in to have what I thought was a throwout bearing quieted down until it was clutch time where it could be replaced at the same time. I was told I may have an input shaft bearing going bad and it would require taking out the transmission and taking it apart for $800 in labor costs. I was also told if it goes out then it may take some parts with it resulting in more money.

Has anyone had this happen to them or can provide more details about this? I'm not going to do it because I don't want to spend $800 on a maybe. It only makes the noise when its cold outside and goes away eventually after driving awhile. I would think a bad bearing would make noise no matter what.

They lubed the clutch fork pivot and end because they said that was making noise but the same noise is still there.

I'm using the Motorcraft ATF that I got from the dealer because I wanted to make sure I was using factory fluid since there seems to be so many theories on what fluid you should use.

I don't know how they can tell its bad just by listening to it from the outside. I'm sure its the throwout bearing or pilot bearing so maybe Ill try somewhere else.