I still think you should give my method a shot, it worked for me. I don’t have it finished yet, its broken up into 3 separate groups, but within those groups all the boxes are sorted and alphabetized from Amazing Spider-Man in the 1st box to X-Men in the last. Part of the reason I haven’t finished it that I like to keep newer stuff separate until I’ve had time to read them.
Start with an empty long box. Open up maybe 3 of your other long boxes. Since they’re already alphabetized it shouldn’t be too bad. Take all the “A”s from those 3 boxes and put them into order in the empty long box. Move on to the “B”s, “C”s, etc. You’ll need to have a couple of empty longboxes to start out with. As you go through the other stacked boxes and interfile more into the “master” boxes, you’ll need to keep shifting books from the 1st box to the 2nd and so on as the contents of each expands, but it’s not as bad as it sounds.