That's a valuable lesson. And I don't mean to sound harsh, because I have been there as well.
Many people get so excited about these projects they just want to dive in. Sometimes that means "winging it" without even having drawings, much less proper patterns. As you have just discovered, however, it's very easy to make simple mistakes that can have profound consequences as you move forward.
With studio-scale projects more than anything else, preparation is vital because you are going to be cutting up potentially expensive kits and making castings of numerous parts (at substantial cost) to glue on your structure. As a result, you should take extra steps to make sure everything fits before you start applying parts.
Many people don't like to bother with a mockup. I hear it all the time. But building a mockup is really mandatory for this kind of project. It allows you to test fit everything. Often you will build a mockup and discover something is off, then you have to revise your patterns and start over. Sometimes this process must be repeated several times until you are close enough to get started building the final model.
As Boba Flint said, even then sometimes it can still be off if you are missing key parts. But as long as you have enough key pieces to lock in the key dimensions, you should be OK if you did a mockup as a "dry run" and tested the fit of everything.
People might think it is too much trouble, but I take the time to do all of the following before I even cut my first piece of plastic:
- Draw my own blueprints.
- Extract patterns from the blueprints to build CG study model.
- Render the CG model from various angles and compare to the original studio model to check for accurate proportions. This includes building CG versions of key model parts to check for fit.
- Adjust CG study model and repeat as many times as needed to arrive at correct proportions.
- Use finished CG study model to create final blueprints and patterns.
- Build a mockup and double check fit.
- Start building final model.
If that sounds like going to a lot of trouble, it is. With simpler subjects it might sound like overkill. The upside is that when I start gluing on expensive kit parts and castings, I already know they will fit properly.
Again, I'm saying this because I sympathize and have been there, so hope it helps.