Hi there, I have a 92 Honda civic DX, 1.5L. When I let the clutch out in neutral a horrible noise comes on. I replaced the throwout bearing that didn't fix it. So I tore it all out again and then replaced the input shaft bearing and its still there. Those were the 2 main things I could think of. I'm not sure what else to do, please help!

 

I assume you replaced part # 12 here:
Honda Automotive Parts
That is usually the problem (a known weakness in these transmissions) but you also need to check the bearing on the other end of the input shaft, part # 9 on this drawing:
Honda Automotive Parts
If there are problems with the internal bearings like #13 #14 etc on the first drawing, it is likely better to swap out the whole transmission. Those should last the life of the car unless abused e.g. by running the transmission without oil.