I think the main problem here is that the gallery, as it stands, is really designed such that all the thumbnails have the same dimensions and the large images are also the same size. That's not the case for you, hence the layout problems (as well as not having the same number of images as in the original).
I'm currently working on a Gallery for a calligrapher, based on this model. If you'd like a gallery like this, let me know and I'll tell you how to set it up (if it's not obvious).
PS The gallery I'm working on is here, in case you're innerested.