Much ugliness! Really could have used better description of the problem, especially where it concerns the other module dependencies. The best I can do is through some psuedo code at you to hopefully get you thinking in a good direction

Basically you need a BEGIN loop to handle your dependencies. The following is real bulky and I have no doubts there are more efficient ways to do this, but I'm just trying to show 'a way' to get you started and it's strictly the first way to come to my head.

/usr/local/bin/perl -w
use strict;

BEGIN 
{
  # I'd put all the locations I want added into an array
  my @inINC = "/pathsToTheModulesIWant";
        
  # I'd load all the current values into a different array
  my @initINC = "/defaultINCPaths";
        
  # Then I'd have an array with all the values I want 
  # pulled from @INC
  my @badINC = "/modules I don't want";
        
  # (With the problems with interdependencies you may need 
  # to move some modules to there own directory )
    
  # I'd then loop through the initial array and load the 
  # paths I want to keep
  my $initPath, $badINCPath;
  for $initPath (@initINC)
  {
    for $badINC (@badINC)
    {
      unless ( $badINC eq $initPath );
      {
        push (@inINC, $initPath);
      }
    }
  }
  # Now that you have the order and values of the 
  # paths you want, set @INC
  @INC = @inINC;     
}

# and On with the programs regularly scheduled execution
use x;
use y;
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Hope this or the criticism arising from this helps!