Help! Small block 360 has a knocking sound

Ok guys, I made a stethoscope and tested all kinds of different spots on the engine for noise. The engine checked out fine. I checked the fuel pump, as you guys mentioned, I checked the valve covers, the heads, none of it was making noise. I even put it on the oil pan just to see if there was anything going on in the bottom end, again, nothing. However, when i crawled underneath and put it on the bell housing, you can hear the knock clear as day, on both sides of the car. I checked the flex plate bolts, all of them are nice and tight. Didn't see any cracks on the flex plate, but there is an interesting thing I noticed, I think there is something wrong with the Transmission. When it is in park, the knock is there, but not very loud. Reverse, it practically disappears, you cant really hear anything at all. Neutral, it is atrocious, the video i recorded at the beginning of the thread was with the car in neutral. In gear, it is just as loud, but when you drive aggressively, it almost seems to go away. Part throttle or letting off the gas, it sounds hideous. I checked the transmission fluid, and for some reason there was almost none in there. Strange because I checked it not that long ago, and it was full. The car doesn't have any leaks that I know of, but I guess it obviously does for the tranny fluid to disappear like that. Didn't get a chance to add more, I don't have any extra at the moment, tomorrow I will get out there and fill the tranny back up and see what happens. Hopefully its not to badly damaged. I feel kinda stupid for running it low on fluid, but the weird thing is that it acted just fine. No slipping or anything, shifted normally as well. If you guys have any thoughts, please share them. Thanks.