@Sonic and Jim
Yep, pretty sure the only answer is the pine has moved more than the ply. I'm a bit worried now that the new pine I have bought is greener than the last lot, so I could be facing the same problem in a about week's time. Oh well, good job its just a hobby that I enjoy.
I think I will take Jim's advice in the future and get some reclaimed wood and try and work with that.
I only have hand tools to build my guitars and leveling off the old body precise enough to take a cap is probably beyond my skills at present so if I do use the old body it will be as it is, which doesn't bother me. Beauty, they say, is in the eye of the beholder. LOL!!