I know by sad experience I'd never leave the trimming and sorting until the end. boring....
I do all scrappy so pin in groups of 10, 10's are so easy to make a quick count. You might sort them into color families?
I gave myself permission a few years ago to not care if like fabric ends up by like fabric and I love how the tops have come out. Not the norm I know, but very freeing and relaxing.
Definitely keep them in a box or zip locks where they won't get tossed around and have a chance to fray once you have them sorted how you like. Good wishes on the project!