Toshi, I built this same kit a couple years ago. I recall having a number of problems fitting some of this detailed interior together. Most of the detail will not be visible at all once you close it up, but if there are any fit problems inside, those will be revealed by poor fit of exterior panels.
That is what plagued my build of the Shinden Kit. I dry fitted everything multiple times and was satisfied that I had determined how everything should go together, but when it came time to glue parts, I did begin to notice alignment problems.
Pay attention to the guns. They may appear perfectly aligned but when you go to fitting the panels around them, that is where you will see a big alignment problem in the way those panels go together. At least for me that was the problem I had, and it was impossible to fix properly.