First of all, this is an excellent idea! I love both vim script and module versions (haven't got the chance to try it, but I will). As for the sequence of functionalities, I'd like to suggest to provide an option to not running the number 4 & 5 (makefile related), as some people writing modules already have a Makefile in their structure, specially if the skeleton was generated with h2xs. I'm talking about the vim script version, as for the module version I believe it is (or can be) more flexible.

I also don't know whether the vim script version requires vim to be compiled with perl or not.