Makes sense. I have color pallet decks, as I typically am the house VJ for festival settings. So I follow the LD in complimentary colors. All the clips in my decks are different without duplicates. If the LD goes from a green to blue without warning, I have only a few seconds to make a smooth transition to maybe a yellow or cyan style clip (could always colorize and do this sometimes as well) but I understand your style of unique clips on unique decks. For me its a matter of realllly knowing my setup. Labelling in alphabetical order worked for me and knowing my clip placement. Having a set of clips for each song (in your case) seems a little more lenient as you probably know the songs well enough to know when it's about to end (not always the case as things can get cut and chopped on the fly haha). But knowing the songs and knowing your decks might give you an advantage over my setup and when you think a song is coming to an end, you can already be waiting for the next song to come up and have that deck already cued.
Do you get a setlist before each show, or does your artist use cdj's?
There is some really cool software that will actually show the current live playlist the artist has cued up and shows the SMPTE playback cursor for each song. This could be helpful to see what he/she has currently cued and is loaded next. Just involves a single ethernet ran from the cdj's to your computer (and the software of course)
I believe the deck switching is getting an overhaul in version 6 but it's going to be a bit before that is released. Just trying to brainstorm to help find you a current solution to your current issue.
All the best