Someone already mentioned that the genes used to make a flagella today had/have other uses as well. Second, while it might take 60 genes today, it might have taken 59 or 58 or 20 several million years ago.
Imo, you have a poor understanding of genetics, mutations in general and protein structure/function. That lies at the heart of your objections. Mutations aren't always single base changes. Read Mark Rs post about the shuffling. Read up on duplications. Entire genomes can be duplicated at once. Clusters of genes can move around. Small portions of genes can be swapped, duplicated or deleted.
While I have no formal training/education in genetics, I can still form an opinion, and I respect that you seem to know more about this subject than I do.
However, your explanation about the genes used to make flagella mirrors the supposed rebukes of Behe's ID that I've read, in that it side steps or glosses over the fundamental difficulties involved in explaining how evolution could create such parts via numerous, slight, successive changes over long periods of time.
This is a very recent article in which the author attempts to show why Behe hasn't been refuted on the flagella.
It's rather technical in nature, but perhaps you could fully understand it.
