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Hi Tim, 1. No, there won't be any negative effect if re directs done correctly(301) 2.There is no hard and fast requirement but I would like to let you know that "Fewer folders is generally better". Thanks

You should definitely be able to ignore these as they're quite common (not specifically these websites, but these types of links). That said, if you are under penalty and can't work out which links are causing it, having cleaned up all the rest, I'd go for a disavowal. If you are 100% certain that the penalty is due to Penguin, approaching the manual webspam team isn't likely to help you at all. But getting that disavowal in before the next Penguin update (which, despite Google's updates of this week - Panda and "payday loans" - can't be far away) might help.

Hi Tim, I think you should do the migration all at once. Make sure you 301 every page or at least the most important ones. This video might help you: https://www.youtube.com/watch?v=r1lVPrYoBkA Magento is great platform, but if not well implement it became very slow. If you 301 your old pages for a much slower page or a page with very different content you might have problems. As long you make sure you content is aligned and your mageto site is fast you'll be fine.

Thanks for your help Tommy