Here's the best I could do at formatting and reading/commenting it, so far:

    ;; Usage: (get)
    ;; Parse the entirety of stdin as a sequence of s-expressions.  Return
    ;; that list of expressions.
    ;;
    ;; The definition of this function is a little contrived, because in
    ;; lisp it's simpler to prepend to a list than to append to it, which
    ;; would be the natural thing to do.  So instead, we build the list
    ;; such that it is backwards, then we call (reverse LIST) on it when
    ;; we read EOF.
    (define (get)
      (get1 (quote ()) (read)))
    ;; Usage: (get CURRENT-BUFFER JUSt-READ-EXPRESSION)
    (define (get1 b r)
      (if (eof-object? r)
          (reverse b)
        (get1 (cons r b) (read))))
    
    ;; Usage: (put)
    ;;
    ;; Read the entirety of stdin as a sequence of characters, perform the
    ;; global string substitution ")" -> ")..", then return the result as
    ;; a string.
    ;;
    ;; The definition of this function is a little contrived, because in
    ;; lisp it's simpler to prepend to a list than to append to it, which
    ;; would be the natural thing to do.  So instead, we build the list
    ;; such that it is backwards, then we call (reverse LIST) on it when
    ;; we read EOF.
    (define (put)
      (put1 (quote ()) (read-char)))
    ;; Usage: (put CURRENT-BUFFER LAST-READ-CHAR)
    (define (put1 b r)
      (if (eof-object? r)
          (list->string (reverse b))
        (if (char=? #\) r)
            (put1 (cons #\. (cons #\. (cons r b))) (read-char))
          (put1 (cons r b) (read-char)))))
    
    ;; Usage: (final LIST)
    ;; ???
    (define (final lis)
      (if (null? lis)
          lis
        (final1 (car lis) (cdr lis))))
    ;; Usage: (final1 FIRST REST)
    (define (final1 f r)
      (if (and (pair? f) (pair? (cdr f)) (eqv? (quote quote) (car f)))
          (cons f (final (cdr r)))
        (if (list? f)
            (final2 f (gather (count (car r)) (cons (quote ()) (final (cdr r)))))
          (if (or (vector? f) (pair? f) (eq? #\) f))
              (cons f (final (cdr r)))
            (cons f (final r))))))
    ;; Usage: (final2 f g)
    (define (final2 f g)
      (cons (append (final f) (car g)) (cdr g)))
    ;; Usage: (count SYMBOL)
    (define (count s)
      (- (string-length (symbol->string s)) 2))
    ;; Usage: (gather c lis) 
    (define (gather c lis)
      (if (= c 0)
          (cons (reverse (car lis)) (cdr lis))
        (gather (- c 1) (cons (cons (cadr lis) (car lis)) (cddr lis)))))
    
    ;; 1. Use (put) to read stdin as a string and perform the ")" -> ").."
    ;;    global string replacement.
    ;; 2. Feed that resulting string to (get), which parses it in to a
    ;;    sequence of s-expressions.
    ;; 3. Feed that list of expressions to (final), which does something
    ;;    to it and returns a list.
    ;; 4. (write) each item that (final) returns.
    (for-each write (final (with-input-from-string (put) get)))