I had similar problems and got myself a pair of these amazing insoles:

http://www.amazon.co.uk/Noene-NO2-2mm-Insole-Size/dp/B000MTF1A8/ref=sr_1_1?ie=UTF8&qid=1338239691&sr=8-1

They're super thin so you can wear them in existing trainers without them overly distorting the size etc.  Honestly though, as soon as I put them in, next run, no pain!  Guy in the shop had a small squash ball sized ball made of the same material as the insoles.  It's squidgy, bt when you throw it at the floor it sops dead, completely absorbs the impact, amazing stuff.  Apparently they use it to line the F1 car seats to reduce vibration.  Anyway, as you can see, I was completely taken over by the sales pitch, but in all seriousness they worked a treat for me.