Ok. The blog is sort of back to normal with all the key links back in place. On the upside I have a slightly better tag cloud.
Along the way I've found out that the new'ish Blogger drag and drop layout tool is ok (and I mean ok, not great), and where services like Feedburner have bothered to create click and play Blogger widgets then getting the links to my RSS feeds back into the template was easy. I've also changed colours slightly for a bit of a change (well, it was easier than trying to change the colours on my new Technorati blog cloud). Actually getting the Technorati link count widget was the hardest part. I should be grateful that at least Blogger lets us fiddle with the HTML if needed (and thanks to Hoctro for the template tip).
But after all this it still doesn't work correctly in IE6! :-( I'm beginning to think that my earlier problems are really just related to my particular install of IE6 and associated security settings (if you're using IE6 does it work for you?) however based on your feedback I'm not going to lose any sleep over it!