Not only had the root damaged the bottom of the boards and broke through the grout, this then allowed the water to travel up the plasterboard making it very weak. The picture above shows how bad its gotten. All the waste got skipped off site giving me a (unlevel) blank canvas to start afresh.
I removed the roots then repointed the wall where it had done any damage. I then started the slow process of battening the walls out to take the plywood. Slow because I want it to be perfectly level to enable easier tiling and so it looks right, the battens before were just fixed straight to the out of level walls and tiles cut to suit which doesn't always look the best.
I did cheat and use plastic spacers which save loads of time (although it's sometimes easier to use folding wooden wedges if you've got the saw set up to make a batch). The plastic ones are useful though as you can increase or decrease the spacing by 1mm just by changing the packer rather than knocking wedges all over the place.
With the external walls insulated its ready to have ply fitted next week and then I can tank it out to make sure its waterproof before I lay a single tile. I've also got to make a new little window for the room so that should be a nice job for a sunny day next week.