Ok, I managed to sort out the fuglies in the blog posts with a lot of help from Mladen over at Wizardworx. A couple important lessons came out of this migration. The first obvious lesson is to make sure you have the right backups before you make the move. We had a mySQL backup (I must just thank Chris Dawson and Andrew Glanville for their suggestions) which the WordPress Backup plugin generated. When we imported this we had a lot of "?" scattered in the text of the posts. I don’t think that is the best solution although I do recommend you install the plugin for emergencies. It turned out that the backup I downloaded from the cpanel on the old site worked far better and this is the version you now see on the site.
Another solution is to use WordPress 2.1‘s export function to export your posts in xml. You can then easily import this into a new WordPress installation. Just make sure you keep a backup of your WordPress installation files (especially your wp-content directory which holds your themes and probably your uploads too). A mySQL backup should preserve most of your settings and formatting (sidebars and users, for example) but it won’t necessarily carry across your uploads (the developers in our audience will be able to tell you definitively) so just watch that.
Anyway, we are back up now. Our apologies for the inconvenience and for the lack of new content the last few days (difficult to add new content it we are going to overwrite it anyway).