awk -F\| '
        {TMP[$2] = TMP[$2] FA[$2] $1
         FA[$2] = FS
        }
END     {CH[1] = 97
         for (t in TMP) {n = split (TMP[t], T)
                         printf "select * from %s %c", T[1], CH[1]
                         for (i=2; i<=n; i++)   {CH[i] = CH[i-1] + 1
                                                 printf " inner join %s %c on %c.%s=%c.%s", T[i], CH[i], CH[1], t, CH[i], t
                                                }
                         printf RS
                        }
        }
' file
select * from Table1 a inner join Table2 b on a.Column1=b.Column1 inner join Table5 c on a.Column1=c.Column1
select * from Table3 a inner join Table2 b on a.Column2=b.Column2
select * from Table4 a inner join Table2 b on a.Column3=b.Column3
select * from Table2 a inner join Table5 b on a.Column4=b.Column4
select * from Table2 a

END     {split ("a b c d e f g", CH, " ")
         for (t in TMP) {n = split (TMP[t], T)
                         printf "select * from %s %c", T[1], CH[1]
                         for (i=2; i<=n; i++)   printf " inner join %s %c on %c.%s=%c.%s", T[i], CH[i], CH[1], t, CH[i], t
                         printf RS
                        }