Few words of advice...(i work at a authorised skoda specialist)
check fuel tank for small shinny metal speckles. Means the fuel pump has basically self destructed.
Depends what type of diesel if its the direct injection PD engine or the other remove the fuel line that goes into the injector and check the injector fuel port for these small metal particles as that would be an issue.
take out the fuel filter doubt you would see anything on it but check the container it came out from and look at the bottom where the left over fuel is for signs of 'badness'. for example small bubbles show water.
You may have changed the low pressure fuel pump in the tank but it may have affected the high pressure pump (if it has one dependant on engine) which is found at the front right of engine, driven by the cambelt.
You may still have the old fuel in the lines thats slaughtered injectors if the fuel lines are metal from the common rail then crack off each one at the injector 1 by 1, retightening before a friend stops cranking the engine, while someone starts so it kicks some fuel out under the pressure... messy job so have a cloth ready but helps get air out the lines or any possible blockages.
If you are struggling to solve then take out the injectors send them off for testing (google search will
help) and get them checked over. Come out easy just undo the retaining bolts and they should gentally yank out. Must stress be careful as delicate and easily damaged, especially the tip when fuel comes out.
Hope some of this helps