Info: I have a 1997 civic HX, stock engine, with an EX transmission swapped in, with now about 180k miles on it. The past few days I've been having a knocking/grinding noise coming from my transmission, it would increase in volume and "speed?" when giving gas, no matter in or out of gear. Tonight something broke and it got a lot louder.

Problem: I would push in my clutch and it would be dead quiet with exception of engine running but it would go off when clutch is out, again with being in gear and in neutral. I cant shift into gear but I floated gears to my house from where it broke. I still have pressure in my clutch pedal, and the clutch master and slave cylinders are both new within the past 1000 miles.

My thoughts: I assume it's either a throw out bearing, but normally is a quiet whining/hissing sound, or it could be input shaft bearings. I would like to know some of y'all's thoughts if you could. Thank you. I also linked a video of me starting my car and pulling my clutch out in neutral:
(alternator belt is misaligned and is making the squealing, will be fixing when my tranny is out)

 

Sounds like you lost the input shaft bearing. When this happened to me about 20 years ago, it also damaged the bellhousing and main shaft.

 

alright, and then for that bearing is it #12 in this diagram?

 

No. It is not shown in the picture you posted. There is a chance it could be any one of the 5 bearings on the main or counter shaft that went out, but it was most likely the ISB. Pull the trans, open it up, then assess what is actually broken.