You will have problems with almost everything when you make geometry like that.
I would suggest starting over using a much looser tolerance
A tolerance of .1 would be better for a model this big. Or you could change the units to meters. Then focus on making simpler cleaner geometry It looks to me that you could make the side surfaces accurately with surfaces that have 20 X 2 control points.
And you should be trying to avoid making surface with multiplicity of knots. Some of your surfaces have thousands of fully multiple knots. If you make surfaces like that you are going to have trouble