Here's another option:

use strict;
use warnings;

local $/ = "//\n";

while (<>) {
    chomp;
    my ( $len, $id, $parts ) = /(\d+)\s+(.+?)\n(.+)/s;
    $parts =~ s/\n//g;
    $parts =~ /.{$len}/p;
    print ">$id\n${^MATCH}\n${^POSTMATCH}\n"
}
[download]

If you're using Perl v5.14+, you can combine the substitution and matching into a single line as follows:

Hope this helps!