(untested)
#!/usr/bin/perl

my %files= ( MainProg2.pl => MainProg.pl, 
 LayerA2.pm => LayerA.pm,
 LayerB2.pm => LayerB.pm,
 LayerC2.pm => LayerC.pm,
 );

foreach (keys %files) {
 open(IN, "<$_");
 open(OUT,">$files{$_}");
 while (my $line=<IN>) {
  foreach (keys %files) {
   $line=~s/use $_/use $files{$_}/g;
  }
  print OUT $line;
 }
 close IN;
 close OUT;
}