My car's been making a chugging noise since I bought it ( almost 2 years ago), please help, what could this be ?

[Fastlife91]

I've had my 2006 ford focus sport 1.8 TDCI for almost 2 years now. I first noticed the car making this noise the day I was driving it home, I had other things on the car to investigate at the time hence why I didn't do much about it .

Anyway, I notice occasionally during idle the car chugs, If I bring clutch up to biting point the chugging goes away, it only chugs occasionally and when it does it is only during idling, I think once the car warms and reaches operating temperature the noise goes away. 

car drives great, even when it chugs at idle but I then proceed to drive it picks up greatly. 

Not the EGR as that has been replaced as well as MAF sensor e.t.c. 

When I first got the car, the injectors did leak a few times but he put a new seal on 1 of them and it began leaking around the leak off pipe but he put a cable tie around each one and have had no leaks since.

 

I would really like some opinions on what this noise could be as I've been hearing the noise since I bought the cart almost 2 years ago  ? 

 

thanks