Looking for help with clipping paths for packaging design.

Hello,

Thanks for reading. I am attempting to create a new sticker label for a new product for my company and I am using assets from a packing file I recieved from our printing/design company. I have attached some screenshots of the issue I'm having. Essentially every little piece of our design, leaves dots etc, are their own clipping path with a square swatch clipped underneath. Since the design is made up of hundreds or thousands of clipping groups, the design is difficult to edit and can't be grouped properly. I am not a pro graphic designer so I am still learning, is this clip group process the prefered method of creating complex designs like this? This is not the process I learned in my graphic design course, it would be more of a stroke and fill object based process to achieve something like this. 

Since everything is in a clip group I can't figure out certain functions to manipulate my file such as "Select>Fill Color" or clipping everything inside my art board using the rectangle clipping mask method pictured in one of my screenshots. I can't clipping mask a bunch of clip groups to a rectangle.

Thanks in advance for any help!