Should i drop my oil and filter and my 1000 mile run in period. After my new engine was fitted?

No not really,

it is a new engine or a Refurbished Engine.

Treat it as a new one.

 

Maybe change at 5,000 miles if you fancy,  

but then Skoda / Dealers say you are supposed to service your car by the mileage.

 

Which is rather daft if it had a new engine , spark plugs, oil and filter a few hundred miles back.

Cheers george