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Personally I like using css layouts instead of tables for many many reasons. SEO isn't one of them.
I believe search engines strip out all the code from your page before determining what ranks where so it really wouldn't make much difference how much code is there from a search engine perspective.
Of course using css to layout the site over tables will likely make the site load faster and make it easier to maintain and to me it's worth it regardless of any affect on seo.
The html to xhtml shouldn't make one bit of difference. I prefer xhtml too since it's the way forward instead of the way back, but it really won't change things with search engines. Similarly for having perfectly valid code. There are reasons to write valid code, but sadly seo isn't one of them.
I think the jury is still out on the effects of css layouts and valid on seo and I know there are still many who insist it's important. I haven't seen it myself and am not convinced there's an seo benefit. I don't think it can hurt though and it's possible it can help. I just haven't seen any real proof of it.
However, I do use all css layouts, xhtml, and validate my code. I don't want to tell you not to redo things. If your current site is coded poorly it can put up barriers to getting indexed. There are coding issues that can help with seo, but you can solve those issues with a css site or a tables based site.
If you post a link to the site in question I'll be happy to take a look at your current code and let you know if I think it needs to be improved.
As for your second question recoding the site shouldn't have any negative effects at all. As long as you keep the same URLs you shouldn't have to worry.
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