So I removed part of the front wheel arch liner.
There was about a pint of damp mud behind the liner and above the plastic sill (see photos).

I hosed it out and dried it off. No rust whatsoever.

It gets in through a gap between the wheelarch liner and the mudflap. Can anyone suggest an upgrade or fix?

Click image to enlarge

Click image to enlarge

I recently fitted a set of steps to mine and found similar amounts.

Having re-installed everything (having given it all a good clean out) I decided to close off all the holes between the mudflaps, wheel arch liner and bodywork with a black silicon sealer. Planning on stripping it all off in a month or two to see if it has worked - if it has I'll do it again.

I found the same initially, fortunately the sills were as new.
Cleaned everything out refitted the liner and then sealed the gap with Gorilla tape.
I also found similar at the backend of each sill.
Cleaned everything out and also sealed the gap between the sill end cover cap and the liner.
I think this particular gap is why the rear of the sills corrode.