I've read through your thread thoroughly and would conclude that the garage you have your car in is run by a complete bunch of non skilled numptys, the very first thing I would do is get the car out of there and to someone who knows and is able to rebuild it, there will be coolant in the cylinders and it will get past the rings and to the sump, but that is the nature of removing the cylinder head, it ALWAYS happens and it can't be stopped, it's why you do a full engine flush following the rebuild.
What I am concerned about is why you thought the head gasket had gone and only at 40000K? The most common thing to fail and cause coolant loss is the radiator, they corrode and slowly tose the fins, then they start weeping and lose cooling efficiency, giving similar symptoms to a head gasket failure and non specialists often mix this up.
You also haven't mentioned which engine this is, TS, JTS, JTD or JTDm? A lumpy idle can be caused by so many things which are simple to sort on each type that you may have dived in too deep too soon.
I think quite clearly here your garage are pulling a fast one, they clearly know that it's not what you think, what they are trying to charge you is the cost of the parts they need to rebuild it and repair the true fault, but any more info on the problem which led to all this would be helpful.
Last thing, if you could put your location up then someone may be able to point youin the direction of someone who can help and I rebuild all of these engine on a regular basis, have over 25 years in the trade and detest the way garages will try to make a fast buck out of the non technically minded.