So, just back from our trip and the Disney Junior Encyclopedia of Animated Characters worked out great! We saw a few other people with the book too, but without the binding modification that I had done.
The book is heavy, which made for transferring between DS (5) and DD (6) to the characters awkward at times. It's just hard from someone their age to handle the size and weight of that book and a marker at the same time. Typically, the kids would take the book to the character, they would sign, give back to the kids, and the kids would hand over the marker and book to either me or my spouse before they posed for photos. Fortunately, I had pre-paid for the Photopass cd, so for any character to which a photographer was assigned, I did not have to worry about taking my own photograph. I'd say there was a photographer for about 60% of the characters we met.
We met about 50 characters, and the only ones that didn't have their own page in the book were:
Princess Tiana
Prince Naveen
Little Einsteins
Handy Manny
(For the four above, I had made pages for them and inserted at the end of the book before I had the book rebound.)
Terk (Tarzan)
Lotso (Toy Story 3)
Mary Poppins
(These three signed blank pages.)
Rafiki (had him sign on Simba's page, where there is a picture of Rafiki and Simba)
We did not get to meet the stars from Tangled, and of course, they are not in the book either.
We used a Bic "Mark-It" permanent market, which was selling at Staples for $0.99 and comes in a variety of colors. There was no bleeding through the pages.