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UUOC! Better directly mail the file:
cmd = "< input.txt mailx -s 'subject' " E[k]
or
cmd = "mailx -s 'subject' " E[k] " < input.txt"

You could do the whole thing in one awk program:
awk '
NR == FNR {
A[$1] += $3
next
}
{
E[$1] = $2
}
...

I don't understand what you are trying to achieve, don't you mean a[$1]+=$3 instead of a[$1]++?