Вот один для awk. Протестировано с GNU awk, mawk, original-awk ie. awk 20121220 и Busybox awk:
$ awk '
function nn(c, b,i) {
if(c)
for(i=1;i<=c;i++)
b=b "n "
return b
}
FNR==1{nf+=(NF-1)}
{
for(i=2;i<=NF;i++)
b[$1]=b[$1] $i OFS
a[$1]=a[$1] (n[$1]<(nf-NF+1)?nn(nf-NF+1-n[$1]):"") b[$1]
n[$1]=nf+0
delete b[$1]
}
END{
for(i in a)
print i,a[i] (n[i]<(nf)?nn(nf-n[i]):"")
}' file1 file2 file3
Вывод:
A 2 3 4 7 6 3 3 2 7
B 3 7 8 n n n 4 7 3
C 4 6 9 2 4 7 n n n
D n n n 1 6 4 n n n
E n n n n n n 3 6 8