While I would need a lot more information or time in your GA to get to the bottom of this, here are some questions:

Did you make any changes to your site code or GA account settings in February?

Did your impressions fall during this time as well or just your clicks?

Are your keywords seasonal, based on specific dates or events?

Do you have an alert in GWMT about your site?

In general structure changes can cause changes in traffic, for your conversion you should also look at your GA goals and how (if any) your events are programmed.

What do you mean "pages that have nothing to do with my site" are these not on your domain or are they on your domain but you are not familiar with them?

Another quick fix would be to use a canonical tag on all of your pages pointing to the full lowercase versions.

So for the URLs example.com/UPPER; example.com/Upper; and example.com/upper you would place the following into the head so Google knows that these are just variations of the same page, and if will point search to the desired page example.com/upper

https://support.google.com/webmasters/answer/139066?hl=en

If the products are all but the same besides color, would you be able to implement something like amazon has, where each product is only one page and you select the color/size option within the the product framework?  This way instead of having a bunch of pages that are basically the same product, all of your effort can go to one page per product.

If you can actually load the regular URL then you should canonical to it (it is best practice to canonical all of your pages to themselves), but if going to that page just redirects to the escaped fragment then you should update how your site build is set up so that you don't have the escaped fragment any more.

While you might see a small down tick in the beginning as Google indexes and updates, overall you should not suffer any long term negative effects from standardizing your URI structure.