Hmm, most of the time i work on one application, and most of the scipts reside in cgi-bin.
When i try to find an older piece of work, the unix command grep is my friend (using it on linux to find specific pieces of code).
Your way of organizing seems fine to me, try grep "your search" -rli from the pwd /perl .
"We all agree on the necessity of compromise. We just can't agree on when it's necessary to compromise." - Larry Wall.