switch($argon) {
my $case = 0; {$IMPUTEinfile="$ARGV[$i]";}
my $case = 1; {$outfilePRE="$ARGV[$i]";}
else {
    help();
}
}
[download]

As for re-writing, try (untested):

if    ($argon == 0) { $IMPUTEinfile = "$ARGV[$i]"; }
elsif ($argon == 1) { $outfilePRE   = "$ARGV[$i]"; }
else  { help(); }
[download]

(But remember that I'm only looking at the "switch" block and guessing; I do not have an understanding of the overall program.)

Update: Normally I'd advise adding the statements
    use strict;
    use warnings;
(see strict and warnings) at the very beginning of the script, but in this case I think you'd end up with so much stuff to fix that maybe the best strategy here really is to make changes at random and pray for the best.