Some (very) rough maths.
High pressure fuel pump is between £500-£600
Injectors seem to vary wildly in price, £150-£300+ with VAT on top, depending on whether you go and which brand you choose.
Timing belt (with water pump kit) is what, around £200
So that's certainly over £1000+ in parts, but let's limit it to £1000 to be conservative for this exercise.
Multiply by 1.9 for (very) rough conversion to Euros = €1900 in parts. (Maybe more, maybe less.)
Labour is about £60-£80/hour, which is €114-€152. (At same 1.9x rate)
Call it €130 an hour.
€3000-€1900 = €1100 labour cost, or a little over 8.4 hours work at €130 (9.6 hours at €114, 7.2 hours at €152)
It's a lot of money, but from my Googling and fairly conservative maths, I'm not smelling a rat here, especially as I've been conservative with the part costs.
I can imagine knocking 25%-35% off that labour cost at an independent, but the parts may be more or less than the numbers I got from Google.
The question is, does all that work need doing? An expert diagnosis of the problem is needed.
Regarding who does the repair work; if you get an independent to do the work, and they don't solve the problem, will they work at no extra cost to resolve the problem? (That should go for the Skoda dealer too.)
Not sure what to suggest, TBH.