I noticed you said you use 'puppy pads' - not sure on the cost of these - would these be more/less expensive than the regular 'blue pads' used for people beds. They come in 2 sizes. I used them for my kitty - Goose. She was old & frail and sometimes had an accident. I went to Wal-mart and purchased a large plastic storage container. I cut the front (one of the long sides) down to about 3 inches, sloped the sides up to the back - put the pads in there for her to use. Such a 'customized' litter box could be cut to accomodate Amy. The sides might help her stand also, once she got in.
Bless you for taking care of a special needs baby