Thought I'd better do an update as its been a while.
Recently had 2 wings, tailgate and a bumper sprayed in the bodyshop. But before they get fitted I had to start on the drivers side sill which was rotten, but not as bad as the other side.
I started by cutting out the the rot on the outer and inner section. The underneath jacking point was bent down to give better clearance.

Shown from underneath, hole around grommet was rotted so this was cut out too.

A piece of steel was cut to fit in the centre section of the sill. This was tacked into place an then zipped up.

The jacking point metal was bent back into place and plug welded to the centre section of the sill. The gap was filled by an angled section of plate.

Rather than by a new sill, I managed to cut a section of sill from another mk3. It had some rust but it was removed with some BH deox gel. It was trimmed to give an exact fit to the cut out sill section.

This was tacked into position, then again zipped up. The welds were ground smooth with a flap disc on a grinder, ready for paint.

No pics of it finished as yet, but the metal underneath was cleaned up and treated with a phosphoric acid solution, then a few coats of epoxy mastic. I then added some brush-on seam sealer and some underbody wax. Cavity wax was used once it was all closed up for extra protection.
Also had to weld up a grommet hole just in front of the drivers seat.

but that's it all done under there now.
Last bit of rust on the rear of the sill to sort and it's off the bodyshop for painting.