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After a preliminary analyis of their setup I found the following that needed to be done:
My question is: Will any of those alterations/additions adjust their current ranking in a negative way?
Instead of totally changing the JS nav, you could place all the JS code in the <head> onto an external file then also make sure every page has a few text links at the bottom for the spiders to follow.
You may find some existing rankings fluctuate, but as long as you clearly present the fact that the client is now gaining MORE traffic/sales/conversions from your work, then the fact that an old page was No.3 but is now No.23 shouldn't really matter, especially if you can demonstrate that the old page was ranking highly for a phrase that didn't actually generate any sales.