It sounds like you have done both of the following for some options, i.e., you've done them both for at least one option:
Used Customize to set and save the option.
Tried to call customize functions to set the option in your init file.
If so, it's you who introduced the redundancy. For a given option, choose one or the other. For example, if you want to ...
I'm not sure why you have both (counsel-projectile-mode) and (counsel-projectile-mode nil) in your .emacs file. Have you tried simply adding a hook to start (counsel-projectile-mode) when loading projectile? Delete (or comment out) the lines you currently have for counsel-projectile-mode and try this:
(add-hook 'projectile-mode-hook 'counsel-projectile-mode)...
As a comment to the answer by wing (but not enough reputation points to comment), org-emphasis-alist is a customizable variable so that it can be customized via the customization menu. It is found in the Org group under the subgroup Org Appearance. Modifications applied via the customization menu should be persistent over sessions.
I think you can use count-words to implement the wc-buffer function and count-words-region to implement the wc-region function - like this:
(defun wc-buffer ()
(count-words (point-min) (point-max)))
(defun wc-region (rbeg rend)
(count-words-region rbeg rend))