How?

ṫø⁹‘‘µFL‘⁶ẋ  - link 1: get the spaces for after the code, dyadic(split string, index)
 ø           - next chain as a nilad
  ⁹‘‘        - right argument incremented twice (the index we actually want)
ṫ            - tail (get the rest of the split string)
     µ       - next chain as a monad
      FL‘    - flatten, get its length and increment
         ⁶   - a space character " "
          ẋ  - repeat the space character that many times

‘ị           - Link 2: get the code for a line dyadic(index, split string)
‘            - increment the index
 ị           - retrieve the string at that index

ḣFL⁶ẋ$;ç@;1ŀ - Link 3: get the code and join with spaces, dyadic (index, split string)
ḣ            - head: split string[index:]
 FL          - flatten and get its length
     $       - previous two atoms as a monad
   ⁶         - a space character, " "
    ẋ        - repeat the space that many times
      ;      - concatenate with
       ç@    - the result of the previous link (the code) - reverse inputs
         ;   - concatenate with
          1ŀ - the result of Link 1 (the spaces after the code)

J’ç@€        - Link 3: a for loop, monadic(split string)
J’           - [0,...,Len(split string)-1]
  ç@€        - the result of the previous link, with revered inputs, for each

ṣ”|Ç;€Y      - Main Link: dyadic(code string, comment character)
ṣ”|          - split on "|"
   Ç         - the result of the previous link
    ;€       - concatenate each with the comment character
      Y      - join with line feeds
             - implicit print