'95 Civic EX 5-speed.

I have a knocking noise coming from the transmission. Does it when starting from both 2nd and 1st and continues until about 10mph or engine RPM reaches 800-1000rpm then just goes away.
Occasional grinding from 1st to 2nd under hard acceleration.
I was wondering what bearing(s) it could be if it is a bearing issue. I did have my input shaft bearing go out and replaced that, when I had the case split at the time the other bearings looked good (year and 1/2 ago).

 

Sounds like a bearing issue, other mainshaft bearing or the outer countershaft bearing is most likely what's bad, but it's impossible to know without pulling it apart.

 

So if it was only knocking in the forward gears but not reverse, would it be a bearing on the counter shaft or main shaft? or could it be either one?