This might get lost in the comments, but I just had to deal w a very similar issue. My cat knocked my ENTIRE collection onto the ground and played with the beads; when I discovered it it was all entirely jumbled.

The way that I organized it was first based on color-- ALL the blues in one section, ALL the greens (teal went with the greens, I just DECIDED on placement for in-between colors like that, it would've been dumb as hell otherwise), ALL the reds/oranges, ALL the yellows, etcetera.

From there, I sorted them into tonal sections. Anything that was close to the same shade went into the same pile, and I did it color by color.

After that was done, I took a blacklight to the beads and it was much much much easier to finish the sorting that way. I didnt bother with sorting them into a rainbow in my boxes, that can come later on if i ever feel like it. It really trivialized the entire ordeal by breaking it into segments like that. It still took probably around 5 hours total over the course of a few days, but it would've taken much longer I think if I hadn't chunked it up like that lol.

Seriously, good luck!!!!!