So far so good - all the rotten wood stripped out and new wood being
cut
ready to fix in to the cut out sections.

Not a method that has ever worked for me. The new bits move and create
gaps where they join the original, and any filler able to withstand that
kind of flexing is too different in texture. Whole sections like cills
are ok but not smaller bits.

What would be the best waterproof glue/sealer to put on the bottom of
the
cill to stick it to the concrete base - I was going to use a
combination of
long screws from the inside and ordinary wood glue to pull the new bits
in
tight which is fine laterally but not horizontally.

I use car body filler for this kind of thing.

Yes best either to bodge with filler and give good paint job, or to do
a proper job and remove/rebuild window.

Thanks - the bits I'm fitting in are just over a metre each which I think
will go in pretty cleanly (hopefully!) with the inner join literally just
under the sliding sash window.

We'll see!

Cheers

Buzby