T(h) 12 I 2 o 4 E 20 N 14 L 1 P(t) 12 I 51 n(S) 5**
r 85 E 20 s 91
6 L 3 P 7 r
y 1(5) d 81
19 O 9 i 19
91(4) C 5 o 14 C 7 T 9 N 2(0) O 51 s 85 i 3 y**
z 81 d 4 n 6 z

There is no need to change the letters.  Just reorder them.  The numbers tell you where to go.

There is no need to reorder the lines.  If you ignore the line breaks, the code is more or less the same (except that letters and numbers would no longer strictly alternate).

The first two letters in the sentence, as you might guess, are "th".