Some interesting points. However, you are assuming a lot for genes in the case of the bacterial flagellum. Genes cannot change themselves. Matter cannot organize itself. A random fortuitous process can be assumed if the chances are reasonable. However when the chances are well nigh impossible then such an assumption is totally unscientific and some other explanation is more likely. The examples used by ID for irreducible complexity or for intelligent design involve systems which are almost infinitely impossible to arrive at by random chance. There are many such systems, and as I often say, yes, it's possible for something which has one chance in an almost infinite amount of chances to occur at random to happen. However, evolution requires many of these almost miraculous occurrences to happen. That makes evolution impossible particularly since no process has ever been found which would reduce the random chances needed to create these systems.
Let me also say one thing about the rocks which are said to be man made. The possibility of these rocks having been formed by some erosive process, by falling and cracking, is more likely than the examples given by intelligent design.
Also the above does not explain abiogenesis - no genes then.
What are you talking about? My post addressed the issue that intelligence was required to manufacture stone tools, and that this information had to be passed on through education...not genetics.