If you want to implement fuzzy string matching, I would look at something like http://arxiv.org/abs/1008.1191 . The experiments look impressively fast.
That was just a fun project, not something I optimized or even tested appropriately.
The theory behind the trie is that the dynamic programming algorithm for Levenshtein distance gets passed to each recursive step, reducing the amount of comparisons needed.
I like this subject so I'm going to read the paper you linked ;)
This is a running issue with fuzzy matching in general, but automatons are especially slow and take forever to build.