Rav 4 intermittent rattle and stall

[knights_in]

Hi all, I am back again for some help with a T180 (2006).

Since I did the Head gasket/EGR cooler the car has been running great; however the last few weeks the car has developed a weird fault. When driving you can sometimes lose power in second/third gear, but you never know when this will happen. I haven't found a common time as it can be on flats and +/- gradients at any time of day/night/engine temp or electrical load.

Just before it decides to stall when idling it has a metal knocking noise that can be removed when clutch pedal is dipped.  Then you get about a minute or two of idling then it will stall and give you an engine warning lamp on the dash. Once you go to restart the car it will crank but not start (No Mil light). Once you have pressed the car ignition button on and off about three or four times it will come into life and purr away albeit with a bit of black/grey smoke for a while. 

I have changed the alternator as that failed a few months ago, the fuel and air filter have been replaced in the last moth. 

The car has been fed Shell for a long time and due to recent events they have switched to Morrisons own diesel but they are going back to Shell once this tank has been used up. 

My thoughts are fuel filter again and/or low pressure pump. But that doesn't explain the Stable idle with rattle that goes with dip clutch.

It had occurred to me to be an EGR valve but that usually throws up a P code that puts the car in limp mode (my experience with it anyway)

Any thoughts or advice is welcomed. Thank you.

[knights_in]

Just an update, the Battery was not able to start the vehicle with 13.2V, but  after a quick charge it started happily.

I am suspecting a ground issue. Last time I had a ground issue on the Battery neg line and that showed up by heavy steering and as I have an intermittent radio (randomly restarts), does anyone know where the wiring loom for the radio is grounded? Or where any of the engine/body/gearbox ground straps are?