Staying injury free for the duration of the 9 weeks was too good to be true after all.
It's strange, but it doesn't hurt to walk, swim, or even run. But when i massage body lotion either side of my achilles tendon, the slightest pressure is very very painful!
After posting a question on this site, and Greg_M making a suggestion as to what it might be i ended up going to a website which I've used for my warm up stretching exercises. This site (http://www.coolrunning.com/engine/2/2_5/196.shtml) had quite a comprehensive list of lower calf injuries which has enabled me to self diagnose.
Now I guess this could be dangerous, but the suggested solution is rest for a few days, followed by running with a heel insert, which cannot cause me any more damage (other than the frustration of not being out running!).
Apparently stretching is also out of the question until the soreness has gone away.
If anyone has had this problem, or can recommend a decent heel insert I'd welcome hearing from them.