g1smd - 1:54 pm on Jan 9, 2013 (gmt 0)
Once all the internal links point to the correct URLs, the next step would be to redirect requests for index URLs to the URL ending with a slash.
If you're not able to do that for a while, as an intermediate step, adding the correct
rel="canonical" tag to each index page would be a good idea.
Tight ship is the only way to do things. :) Never let search engines guess what you meant.