I seriously think you have been taken for one heavy ride mate.

I take it it is out of warranty ?

Plugs and leads could have been easily checked by doing a simple resistance check on them to see if one was faulty / breaking down.

Coils dont generally phase out to cause problems - they either work or they dont.

Wiring looms - all the wires inside it are protected with outer sleeves are they not. Unless you had a constant drip of water pouring over joins all day long they are built to with stand damp. Most plugs used in the engine bay are weatherproof either outside or inside.

They didn't have a clue what the problem was IMHO and are going round in circles looking for it at your expense.

After the first payment was made you should have got confirmation that the fault you brought the car in for had been fixed. That way you have paid to have the fault fixed, anything else needed subsequently should have been at their expense as they didn't do the job you asked.