my @val = split(" ",$val);
my $v = join (":", @val);
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Assuming that you've already made sure that $val contains only the fields that need to be delimited by colon instead of whitespace, you could just do this:

$val =~ s/\s+/:/g
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As for the other snippet, you could use a hash of arrays instead of a hash of concatenated strings, then join the array elements for each hash key after the whole set has been loaded. Here are the relevant loops (with a few other changes):

my %hash;
while (<DATA>) {
    s/\s+$//;   # remove all trailing whitespace (not just newline)
    s/(\S+\s+\S+\s+)//;  # remove (and capture) first two fields
    my $key = $1;
    s/\s+/:/g;  # join remaining fields with ":"
    push @{$hash{$key}}, $_;
}

foreach my $k (sort keys %hash) {
    print $k.join( ', ', @{$hash{$k}} )."\n";
}
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There's nothing wrong with the way you originally did it - it works, it's clear, it's not wasteful, and that's all good.