Thank you for hanging in on this one. We may have a perfect storm of more than one issue.
I think the earlier suggestion of a dodgy plugin may be true after all. I've been monitoring how Logic has been performing while working on a new song. The delay problem suddenly arose when I set up a cracked plugin on one of the tracks. Strangely, the damage seems to be irreversible, because when I removed the plugin again, the problem remained (this confused us earlier).
The moral of that tale seems to be 'buy the real thing!'which I will do.
Logic not replacing the preferences is a strange one isn't it? (I did keep the plist safe, so was able to replace it and get sound back again. Phew!) Maybe I SHOULD just re-install Logic. It will be interesting to see if it will then be able to create a new preferences folder. After Christmas, I'll try the project on a friend's Mac too. We just have to be painstaking and thorough with this one!
Thanks again for your stalwart support. Have a lovely Christmas and only solvable problems in the New Year!