I use Paint.Net and copy the parts I need from a sprite sheet from spriters-resource.com. So I don't know much about aligning, but I mostly use the images that you have made and overlay them with the parts. I shall look up GIMP and see if I can alter it.
*Edit*: I have remade the Dreamshrine in GIMP, I have had to make some changes, but I hope it is better now. If there is still something wrong I have added the place where you can get the xcf file as well. I will look at the Phonebooth somewhat later. I'm sorry about the mistake, it is my first time I sprited something.
[imgzoom]http://home.student.utwente.nl/n.j.hoeijmakers/LAGB/Dreamshrine2.png[/imgzoom]
*Edit*: A new version of the phonebooth. I hope you like it, the xcf file can be found in the same directory below.
*Update*: I didn't feel like getting to work yet, so I made Ulrira's House. I've used GIMP with a raster of 16x16. I hope it is usable for you. Again the xcf file is downloadable from the directory.
directory with images