> For one, I never really got it working.

If you can't get something like Shiichan working, what are you doing trying to write your own board software?

> I don't know the advantages of PHP over Perl but as far as I can tell it seems like the majority of newer scripts are written in PHP.

Quantity != quality. Popularity != excellence.

The majority of code used to be written in BASIC too, back in the early 80s. Did that make BASIC better than, say, C, Lisp, or Forth?

Perl is a far more powerful language, and faster and more secure to boot. The learning curve is far higher than PHP's though, which results in the current situation.