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Please check the development versions area. Look at the changelog, maybe your specific problem has been resolved already!
#6567 – Prevent canonical url generation
You probably should have kept using sh404SEF at the time: this poor canonical was not added by sh404SEF but by Joomla itself. It was pretty bad indeed, to the point we had to add a feature to remove it:
Joomla does not do that anymore now however. As for sh404SEF, it basically does not insert canonical links automatically, except in one case, and never did.
The only exception is for Joomla articles: when on the canonical URL, we do insert a canonical to that Joomla article.