How to debug a(n) .emacs that doesn't work correctly, but also doesn't throw any errors?

Question

I currently have an Emacs/AucTeX setup where emacs --debug-init doesn't throw any errors, but things still don't work as expected. This being the case, I don't really know how to debug my .emacs file without endlessly shuffling lines around, etc.

Two examples of things that don't work as expected:

• Although I have activated reftex-isearch-minor-mode (C-h v says it's t, although the status bar doesn't show it's activated), it only works if after emacs has started, I deactivate, and then activate the mode again via M-x.

• I have activated electric-pair-mode, and in a multifile-document the following happens: Typing (, [ or { in the main file results in emacs inserting a pair as expected, but typing [ in a non-main file (?) only inserts a single [, while ( and { are still inserted as pairs.

So, my question is: How can I get my setup to work correctly, or can someone point me at a resource that tells me how and in what order I have to put in the various setq, require, and whatnot lines, so that everything is loaded and hooked correctly.

Disclaimer №1: I have practically no Lisp knowledge (and I fear it shows…).

Disclaimer №2: I first asked this question on tex.se, but was told it's more appropriate to post it here.

My .emacs (that is probably a bit messed up) for reference:

;; Added by Package.el.  This must come before configurations of
;; installed packages.  Don't delete this line.  If you don't want it,
;; just comment it out by adding a semicolon to the start of the line.
;; You may delete these explanatory comments.
(package-initialize)

(setq package-archives '(("gnu" . "http://elpa.gnu.org/packages/")
                         ("marmalade" . "http://marmalade-repo.org/packages/")
                         ("melpa" . "http://melpa.milkbox.net/packages/")))

(load "auctex.el" nil t t)
(load "preview-latex.el" nil t t)

(setq-default TeX-master nil)
(setq TeX-parse-self t) ; Enable parse on load.
(setq TeX-auto-save t) ; Enable parse on save.
(add-hook 'LaTeX-mode-hook 'visual-line-mode)
(add-hook 'LaTeX-mode-hook 'flyspell-mode)
(add-hook 'LaTeX-mode-hook 'LaTeX-math-mode)

;; Enable RefTeX automatically in AUCTeX buffers.
(autoload 'turn-on-reftex "reftex" "RefTeX Minor Mode" nil)
(add-hook 'TeX-mode-hook
      (lambda ()
        (turn-on-reftex)))
(setq reftex-plug-into-AUCTeX t)

;; AUCTeX-related settings.
(add-hook 'LaTeX-mode-hook
      (lambda ()
        (LaTeX-add-environments
         '("satz" LaTeX-env-label)
         '("lem" LaTeX-env-label)
         '("Bem" LaTeX-env-label)
         '("Bsp" LaTeX-env-label)
         '("Def" LaTeX-env-label))
        (add-to-list 'LaTeX-label-alist '("satz". "thm:"))
        (add-to-list 'LaTeX-label-alist '("lem" . "thm:"))       
        (add-to-list 'LaTeX-label-alist '("Bem" . "rem:"))
        (add-to-list 'LaTeX-label-alist '("Bsp" . "exp:"))  
        (add-to-list 'LaTeX-label-alist '("Def" . "def:"))))

;; RefTeX-related settings.
(setq reftex-label-alist
      '(
    ("satz"   ?T "thm:"  "~\\ref{%s}" nil ("theorem"   "thm."))
    ("lem"   ?T "thm:"  "~\\ref{%s}" nil ("lemma"   "lem."))
    ("Bem" ?R "rem:" "~\\ref{%s}" t   ("remark" "rmk."))
    ("Bsp" ?E "exp:" "~\\ref{%s}" t   ("example" "exp."))
    ("Def" ?D "def:" "~\\ref{%s}" t   ("definition" "def.")))
    reftex-insert-label-flags '("s" "sftTRED"))

(require 'org-table)

;; auctex-latexmk
(require 'auctex-latexmk)
(auctex-latexmk-setup)
(setq auctex-latexmk-inherit-TeX-PDF-mode t)

(setq TeX-source-correlate-mode t)
(setq reftex-isearch-minor-mode t)

(add-hook 'LaTeX-mode-hook (lambda ()
                             (TeX-fold-mode 1)))

;; Markdown-Major-Mode
(autoload 'markdown-mode "markdown-mode"
   "Major mode for editing Markdown files" t)
(add-to-list 'auto-mode-alist '("\\.md\\'" . markdown-mode))

;; Pandoc-Minor-Mode
(autoload 'pandoc-mode "pandoc-mode" "Minor mode for using Pandoc" t)
(add-hook 'markdown-mode-hook 'pandoc-mode)

;; turn on automatic bracket insertion by pairs. New in emacs 24
(electric-pair-mode 1)

(setq TeX-electric-math t)

(add-hook 'plain-TeX-mode-hook
      (lambda () (set (make-variable-buffer-local 'TeX-electric-math)
              (cons "$" "$"))))
(add-hook 'LaTeX-mode-hook
      (lambda () (set (make-variable-buffer-local 'TeX-electric-math)
              (cons "\\(" "\\)"))))

;; turn on highlight matching brackets when cursor is on one
(show-paren-mode 1)

;; (setq show-paren-style 'parenthesis) ; highlight brackets
;; (setq show-paren-style 'expression) ; highlight entire expression
(setq show-paren-style 'mixed) ; highlight brackets if visible, else entire expression

;; The library uniquify overrides Emacs’ default mechanism for making buffer names unique 
(require 'uniquify)

(custom-set-variables
 ;; custom-set-variables was added by Custom.
 ;; If you edit it by hand, you could mess it up, so be careful.
 ;; Your init file should contain only one such instance.
 ;; If there is more than one, they won't work right.
 '(TeX-PDF-mode t)
 '(ansi-color-names-vector
   ["black" "#d55e00" "#009e73" "#f8ec59" "#0072b2" "#cc79a7" "#56b4e9" "white"])
 '(custom-enabled-themes (quote (zenburn)))
 '(custom-safe-themes
   (quote
    ("67e998c3c23fe24ed0fb92b9de75011b92f35d3e89344157ae0d544d50a63a72" default)))
 '(ispell-dictionary "british")
 '(package-selected-packages
   (quote
    (zenburn-theme auctex-latexmk cdlatex org popup pandoc-mode markdown-mode csharp-mode)))
 '(reb-re-syntax (quote string)))
(custom-set-faces
 ;; custom-set-faces was added by Custom.
 ;; If you edit it by hand, you could mess it up, so be careful.
 ;; Your init file should contain only one such instance.
 ;; If there is more than one, they won't work right.
 )