All of the 'special cases' in the first post are not included, so all of those should be missing (ship_2 is also not there, forgot to add it to the list). I was not aware of naming issues. Palmer does a pretty good job at importing/exporting, but it is definitely not perfect. The biggest problem at the moment is the lighting problem, which I know how to fix, but it will just be a pain in the ass to re-process everything and release again. It will come, but it will take a bit. For now, do what you can to make it playable and things will improve as myself and the other field people work it out.
yarLson, I don't think you should end your project, but you can use the script to move quickly through all the files. Most will not need any touchups at all and that will save you tons of time. The others should have many of the field files looking fine but only a background or an animation to touch-up, saving even more time. In the end, I think it is your effort that will produce the most refined final product that we are working towards. FacePalmer was really meant to get something out that people can play asap because that gets more people interested.