For months and thousands of miles now, I thought the obvious and loud noise coming from my 96 Civic EX (D16Y

was the throw out bearing, and I disregarded it.
But recently I read up a few things and it turns out to be the input shaft bearing, which is apparently a little more serious than a throw out bearing.
The thing is, the noise doesn't always sound. If I accelerate just right in first from a dig, and shifting from first to second, the noise doesn't occur, and it sounds as if there's nothing wrong with my car. It's always done this, ever since the sound started happening.
Now I really don't know what to do. I changed my transmission fluid tonight. That helped shifting, but the sound is still there. Should I rebuild my tranny? Or find a replacement?
I'm open to any suggestions, advice, and input in general. Also, I'm apparently looking for a D16Y8 hydro tranny, lulz.
Thanks guys