#!/usr/bin/perl -w
use strict;

my $in ="20120704 00:05:53.46;CmdTask(0);EV;FBLdxPreAlignment rtn=0, Yoffset=-4278   ";

#desired: 20120704,00:05:53.46,,,-4278 

my ($num, $time, $offset) = $in =~ /\s*(\d+)\s+([\d:.]+).*=([-\d]+)\s*$/;

print "$num,$time,,,$offset\n";
__END__
prints:
20120704,00:05:53.46,,,-4278