couple of basic things.
the cap on the intercooler radiator is lower rated than the main one at the back of the engine bay. just check if it opens water can't go anywhere. it really should have a blanking plate there as its not meant to be used. i can't tell if it has an overflow bottle fitted.
the main cap at the back of the engine bay is down to low. that should be the high point. the bonnet should be hitting it. having it low risks trapping air in the IC.
those IC's are difficult to get all the air out at the best of times.
the pump should be the low point. it wants to be under the radiator or along side the bottom outlet of the radiator. it should also be pumping to the high point (the cap at the back) not to the IC.
so water circuit should be pump (low point) to cap (high point), down to IC, down to radiator, down to pump.
i can't see how big the IC radiator is. one of the big issues with those kits is they are meant for petrol's and typically come with small radiators. with diesels you need the biggest radiator you can possibly fit. i know its tight space in there so you may have the biggest you can practically fit.