Hopefully this will be of use to someone.
I had two main issues, some water (1-2cm deep) in spare wheel well and a strong smell of exhaust fumes when driving with the window open.
Water in wheel well
After removing all of the panels in the boot (thanks to Total Technik videos on YouTube for instructions) there were 2 causes. First was a leaky wiper motor. I replaced it with a genuine item from Amazon (£60), this fixed the issue.

The second was a load of crud collecting under the plastic panel which runs along the top of the boot, effectively sealing the roof and the boot lid. I pried this off and found a load of mud / leaves / water. After clearing this out, and fixing the wiper motor my boot is dry.

Fumes
The issue was only noticeable when a window was down (or the sunroof open). The smaller the opening the stronger the smell. Again, there were two issues. One was the boot seal was not glued all the way around, most obviously around the rear light clusters. Using some Tiger Seal (£6 from Eurocarparts) this was easily fixed. The second took longer to find. Basically there are 2 air pressure vents which help reduce pressure in the car when doors are opened / shut etc. These can be found inside the car, below the rear lights (easy to see on the passenger side but the BOSE amp needs to be removed on the driver’s side). The seal around these had perished, creating a small gap. Makes sense when thinking about it. The greater the vacuum created by the smaller opening in the passenger compartment the greater the ‘pull’ from these vents. Given their location just above the exhaust all of those fumes were making their way into the car. I found some on eBay for about £15 each.


As I said, I hope this is of use to anyone experiencing similar issues, please feel free to message me and I will try and help where I can.