Hey damonjynx,

What you want is possible in the CC 2018 version, but it might as well work in CS4. Here's how I did it. It basically involves making a clipping mask, expanding the shapes and cropping. You should probably work on a copy of you art - preferably in a separate document - and when you are done, just copy the resulting shapes and paste them to your original document.

- Make sure the red shape is on the topmost layer (you can move it to a layer of its own and drag this layer all the way to the top). This shape will be used as a mask and will be destroyed in the process, so make a copy if you want to keep the red border.
- Select the red shape and all the objects that should be inside the box. I think select all might work here too.
- Menu > Object > Clipping Mask > Make. At this point, only what's inside the red square should be visible; but the rest of the shapes are still there, just masked out. Without touching anything (ie. select, deselect etc.), perform the next 3 actions.
- Menu > Object > Expand Appearance (if available)
- Menu > Object > Expand
- Menu > Effect > Pathfinder > Crop (or click the Crop icon in the Pathfinder panel)
- Ungroup the resulting objects if you want

Again, this has worked in my AI version, so give it a try. Otherwise, you can google "illustrator clipping mask crop" and see what you will find.

I hope it helps.