Citigo clutch replacement SKODA CITIGO

clutch failed mid-journey, preventing acceleration and causing burning smell. When mobile mechanic removed clutch, they saw it had completely worn out, and had made mess inside engine. Thus replacement took longer than expected, and they charged more than quote. 

Replacement clutch now needs to be primed, hard to get into some gears. Mechanic said they were aware, and caused by either slave or master cylinder, aren’t sure which, will replace for extra charge. 

Knowing little about cars, I want to ensure this is reasonable chain of events, + check how much we should expect them to charge for the master or slave replacement. Should the slave have been included in the original clutch kit replacement cost?