#!c:\perl\bin\perl.exe -w

use strict;
use warnings;

for my $line (<DATA>)
{
    $line =~ s/ \d{4,}( |$)/ 0$1/g;
    print $line;
}

__DATA__
1125356700 0 0 0 0
1125356400 15 0 25 0
1125356100 25 0 25 0
1125355800 25 0 25 0
1125355500 25 0 25 0
1125397800 0 0 0 0
1125397500 0 0 0 0
1125397200 0 0 0 0
1125396900 0 0 0 0
1125396600 0 0 0 0
1125396300 0 0 0 0
1125396000 39006 0 63597 0
1125395700 63597 0 63597 0
1125395400 63597 0 63597 0
1125395100 63597 0 63597 0
1125394800 63597 0 63597 0
1125394500 63597 0 63597 0
1125394200 63597 0 63597 0

##</code><code>##

perl.exe -ple "s/ \d{4,}( |$)/ 0$1/g" filename

##</code><code>##

$line =~ s/ (\d+)/$1>1000?" 0":" $1"/ge;