Estimation should be independent of whether you will use Perl. See Function point analysis and COSMIC, for example. For project management, we use Rational Portfolio Manager, RequisitePro, ClearCase and ClearQuest, but there are very good libre projects that do what some if not all of these do. I don't do contract work, so I can't give you an hourly wage feedback. The wages are likely to vary wildly from country to country. Cheers.