Yes, you are on a good way. The problem is that you perform the substitution on even lines in the input:
NR%2==0
Removing the check should fix the issue:
awk 'BEGIN{split("5 6 7",a," ")}{t=$0;sub(/.$/,a[++i],$2);$0=t RS $0}1' FS=\" OFS=\" /tmp/MC/Cell_F1 > /tmp/MC/Cell_F2