Ok here is something to consider that produces your output to the best of my understanding at the moment:

#!/usr/bin/perl
use warnings;
use strict;

# this uses a "trick" to open an in memory file
# like a file on the disk for testing purposes

my $file1 =<<END;
1 19002930  0.74
1 19002931 -0.12
END

my $file2 =<<END;
1 19002930 0.84 0.12 0.94
1 19002931 0 -.20 .12
END

open (my $fh1, '<', \$file1) or die "$!";
open (my $fh2, '<', \$file2) or die "$!";

my $lineFile1;
my $lineFile2;

# compare line by line of both files
# stop if either file "runs out of lines"
# assumes that say: line 232 of file 1 goes with line 232 of file 2

while (defined ($lineFile1=<$fh1>) and defined ($lineFile2=<$fh2>))
{
   my ($line1Col1, $line1Col2, $line1Col3) = split ' ', $lineFile1;
   my ($line2Col1, $line2Col2, @file2rest) = split ' ', $lineFile2;
     
   if ($line1Col1 == $line2Col1 and
       $line1Col2 == $line2Col2)
   {
      print "$line1Col1 $line1Col2 ";
      print join" ", grep{ $_>=$line1Col3 }@file2rest;
      print "\n";
   }
    
   else
   {
       # col1 and col2 didn't match, so we do nothing
       # you can delete this else clause entirely
   }
}    

__END__

prints:
1 19002930 0.84 0.94
1 19002931 0 .12
[download]

Could be written shorter, but I think that this what you want and it will run very quickly (compared with R).