I'm currently running:
  Activestate 5.6.0 build 623
  Apache 1.3.19
  mod_perl 1.25
under Windows 98... and it works!

Most of the difficulty of this "Perls before sWine" kind of configuration is handled for you by randy kobes. All you need is basically a 5.6 Activestate Perl, a post 1.3.12 Apache, and the instructions at ftp://theoryx5.uwinnipeg.ca/pub/other/ActivePerl.readme, which boil down to using ActiveStates's Perl Package Manager:

  ppm install
    http://theoryx5.uwinnipeg.ca/ppmpackages/mod_perl-1.xx_1.3.yy.ppd
[download]

I haven't ever used IndigoPerl, but I've generally been pretty happy with ActiveState, as happy as you can be working under Windows, trying to pretend it's Unix... Good luck.