You can put a record in each line an then use split to get single records:

#!/usr/local/bin/perl
use strict;
use warnings;
use Data::Dumper;

my $text = do {local $/;<DATA>};


$text =~  s/\n(?!\d{7})/ /g; # Remove newline if no
                             # new record

my %records = map { split /\s+/, $_ , 2 } split /\n/, $text;

print Dumper(\%records)

__DATA__
1000001 01.11.199600.00.00001 A1 1 SN Y
2001.11.200400098.0500073.5500083.35
5001.11.1997Professional attendance being an attendance at
5001.11.1997other than consulting rooms
1000002 01.11.199600.00.00001 A1 1 SN Y
2001.11.200400098.0500073.5500083.35
5001.11.1997Professional attendance being an attendance at
5001.11.1997consulting rooms
[download]

Hope it helps,
deibyz