How to migrate from Commerce Kickstart to Drupal Commerce?
tl;dr - Essentially, you're building a new theme on top of a site that is populated with content:


  
  Find or create a new sub-theme (that doesn't use omega_kickstart as a parent).
  Create a new home page.
  Create new blocks for menus and taxonomy terms.
  Re-implement any social features you were using.
  Examine and fix any order, user, or content related problems.
  Enable the new theme and configuration.
  Disable all of the kickstart modules.
  Test and repeat until you're happy with the results.
  


More information:

Let's say you disable all of the Kickstart-specific modules by running these commands: 

drush -y dis commerce_kickstart_block commerce_kickstart_blog commerce_kickstart_comment \
  commerce_kickstart_inline_help commerce_kickstart_menus commerce_kickstart_merchandising \
  commerce_kickstart_order commerce_kickstart_product commerce_kickstart_product_ui \
  commerce_kickstart_reset commerce_kickstart_search commerce_kickstart_slideshow \
  commerce_kickstart_social commerce_kickstart_taxonomy commerce_kickstart_user


And then you can disable the other modules:

drush -y dis commerce_kickstart_help commerce_kickstart_migrate


Here's a picture of what your site's homepage will look like if you afterwards (assuming you're still using the same base theme):



You'll find that:


All of the home page content is gone.
The menus are gone.
The admin menus are damaged but usable. (There appears to be a one-pixel line at the top of the page that allows you to click on menu items unless your screen is extremely wide.)
All of the theming done for products is gone.


The good news is that:


All of your content is still there.
Links to existing products will work (albeit not as pretty).
Administrative functionality is A-okay.


Given the current situation, you'll probably want to go ahead and create a new theme. I suppose you could sub-theme the existing theme, but I'm not sure why you would given that everything is now broken.

The homepage will also need to be replaced. Views, panels, or a node would all be good choices, depending on your needs. The rest of the blocks and menus will also need to be created as blocks and re-added to your theme, but you'd need to do this anyway so it's probably not a big deal.

Any other customizations around comments, users, orders, etc. will need to be reevaluated and implemented as you see fit.

Once you're happy, you'll just need to test, test, and test some more to make sure you've cleaned up all the edges.