Today was the day! After removing the pipes with the heat exchanger in situ it was very clear that the unit was going to have to be removed and inspected properly.
Bringing it out of the boat I removed the end caps to see the extent of the build up
As for cleaning it I went with Beamishken's suggestion of the ebay brick cleaner and it is wonderful yet frightening stuff. I put one end of the unit back together and a bung in the outlet. I placed the whole shebang in a builders bucket and poured away.
Its amazing how fast this stuff works. Make sure you are outside and have full protective gear on. It bubbles up very violently and you can see a lot of vapour coming off so I would suggest you stand up wind. I am very impressed with the results and as he mentioned it only took 5 mins. One 5 liter drum was more than enough to complete the task.
Next stop the intercooler!