The only thing I change in the .xml is the name of some actions, which is pretty much irrelevant.
I believe the image anchor is based around ratio rather than the actual canvas size which means editing size isn't based strictly on what it says in the file.
By "line it up", I mean, I drew a part of the shimeji I wanted in a certain place (mostly the head in this case) and saved that. I then made a new file with a bigger canvas and copied the old head onto that one (I use SAI so it pasted into the same place it was on the other one) and then drew around it to make the rest of the shimeji. Because the head (and therefore the rest of the shimeji) was in line with the other files, it fitted in just as a 128x128 canvas would have.
I understand the .xml and anchor points and that sort of thing, I know what you mean.