Grinding noise when engine braking in low gears and reverse [When Cold]

Hi, I have a FD1 Civic and about 2 months ago my clutch pedal and slave cylinder started squeaking. I tried spraying white lithium grease into the hole (direction from online) and it only worked for a day and then it came back. This isn't the worst until I found out there's grinding noise, possibly from the clutch/transmission. I don't think the squeak and the grinding noise is related. Anyways, when I'm reversing (Cold start in the morning then reversing into the driveway) and engine brake on 1st and 2nd gear (I don't usually engine brake on these gears but it will 100% make this noise when it's cold) it will make the grinding noise. The car drives perfectly fine but makes a obvious grinding noise when it's cold, and after 15minutes of driving it is completely fine and even starting again throughout that day. Noise comes back the next morning. Does anyone have similar issues or can lead me to the correct direction? Transmission fluid has been changed in Dec 2015 and I will check the fluid level tomorrow morning.

07 Civic, 130K on the clock

Overdue for a gearbox service

Sounds like the gearbox main shaft bearing

Yeh tested it again just then, definitely goes away after 15mins of driving. How much will the fix be around for gearbox main shaft bearing?

Update # Ok it might not be a grinding noise but more of a clunk sound because everytime I go past bumps it makes that sound too. The small vibrations from the engine brake is probably triggering the grinding/clunk sound. Might be the sway bar links that needs changing. I'm going to get it changed and then i'll update back next week

You might be able to get a better quote from your dealership if that's where you're bringing the car for servicing. You can also try getting a good quote at the other workshops around your area. I would also try not to push the car too much until you get it fixed. It sounds like your running it more ragged testing it out to check out what the issue is, but that's just my take.

IMO since its a manual, just change the fluid and drive the thing till it breaks. How expensive can an ecobox's gearbox be.

I wouldn't be taking it into any dealerships, instead go to a well known gearbox rebuilder and letting him tell you what it is. Worse case scenario is couple hundred for working gearbox from the wreckers.... its not a type R box so it will be dirt cheap. Heaps cheaper then rebuilding for sure.

Yeah I agree amant,I mean unless you do the Labour yourself it's gonna be $8-900 give or take just for Labour. The gearbox must be dropped if It is the gearbox. ..do you think it may not be now?

I just did that graphite grease on the pivot ball for the clutch. Take off the slave cylinder and grease the ball hiding inside the rubber boot.Good to bleed the clutch and remove any trapped air in the clutch line.A hand pump works best I reckon.

Ok I found out the vibration noise. It's the engine mount which happens when engine braking and reversing.

http://imgur.com/a/mmWDt