Anyone know where I might get pick up sills from?

no chance

they haven't been available to buy from skoda for a long time.. plus most of the mainstream panel suppliers only do them for the hatchback models

You could try VW and see if they do them for the old VW Caddy pickup (A rebadged felicia pickup), otherwise cut out the dud section and you'll need to get a piece of metal made up to fit the hole as my brother did on his felicia estate.

Could I modify hatchback sills withut too much bother? Surely the main outer sill is the same or v similar, the front door aperture will be the same, just need to loose the rear door aperture bit? Anyone done this?

the hatchback sill are too short!

I need some sills too are estate ones any good

Estate and hatch are the same between the wheels aren't they? The extra in the estate is in the rear overhang I think.

I successfully modified and fitted a pair of hatchback sills to my truck. Cut out the bit where the door should go, wallop, pick up sill! Same length as hatch.