G'day reaper9187,

Here's my take on a solution:

$ cat fred.dat
"A","B","C","D"
"A","B","C","D,E,F"
"A","B","C","D"
"A","B","C","D,R,T"
[download]

$ perl -Mstrict -Mwarnings -E '
while (<>) {
    my ($start, $end) = /^(.+?)("[^"]+")$/;
    my @finals = split /,/ => substr $end, 1, -1;
    say $start, q{"}, shift(@finals), q{"};
    say q{ } x length($start), q{"}, shift(@finals), q{"} while @final
+s;
}
' fred.dat
"A","B","C","D"
"A","B","C","D"
            "E"
            "F"
"A","B","C","D"
"A","B","C","D"
            "R"
            "T"
[download]