1.6 TD Passat 1987 Transmission grinding issue

[33B]

So i changed the transmission on my car. I found one in a really good condition, almost no wear on it. But after fitting the trans. and draining all the oil (no metal in the oil) I poured in only 1l of oil and it started coming from the fill plug, and the manual says that it takes 2.1l. I went with it anyway.
On first startup some type of grinding could be heard upon releasing the clutch (about half way), something like a metal rattle. But after driving it for a bit it started doing that loud metal clatter on idle. As soon as you press in the clutch it stops, or if you bring up the revs (rattles around 900-1000 rpm anything over that no problems). Also when creeping in first gear without throttle it does the same thing so its rpm related. Could it be the input shaft bearing? I've researched a bit and all of them have that rattle in all the rev range, sound maybe changes but its there for them. I dont have that issue.

So my question is could it be due to low gear oil or is it really the input shaft bearing. Thanks.

[ORCoaster]

I recently changed the oil in my transmission and I pulled the lower plug and got out what looked to be about two liters of fluid.  I then pulled the reverse switch out and refilled it with the recommended ounces from there.  I don't like that side fill plug at all and never use them.

I would try to get more oil in that transmission and see if that gets rid of the metal sounds.  That can't be good for those internal parts. 

[33B]

I was actually thinking to fill it from the breather up top, but r light switch idea isnt bad.
Thanks for the reply.
From the research I did the clattering sound is actually throw out bearing. Because sound doesnt change/ increase with rpm but disappears. It seemed fine when I was fitting the transmission, I put in a used new luk clutch plate and pressure plate, throw out bearing when looking and spinning it seemed fine (although i did find numbers 87 stamped on in, i guess its the original th. bearing). That's what I deserve when I could buy a th. bearing new for 10bucks..
By new used I mean its been fitted to another car but has not more than 500km on it. Simply didn't have money after buying a used trans and 1.6TD engine, but was very lucky to find that it was a conversion from gas to diesel. And someone converted it drove it for a few years and junked it because the body was rotten. (Engine and trans have about 100k km on them more or less nothing)
And also a small humming, like a rally car noise, coming from the transmission is due to low and improper oil. Very hard to find exact info about oils for these old cars. I have finally found it on some Russian forum after hours and hours of research (google translate ) and it takes 80w 90 GL-4. Although it's for the Audi 80 b2 (audi 4000 for you US folks), but this Passat is the same under it's skin as Audi, being made on that platform. Only difference is body panes and rear axle beam, on passat its a stronger beam due to it being produced few years later and had that upgrade. I put in 75w-90 and it being synthetic is most likely the reason for that slight hum.