I've solved the problem: I unchecked Generate World Map Size and it seems to be scaled properly now.
This image probably makes absolutely no sense visually, but it shows that everything is now to scale. The blocks sticking out are actually punch blocks I'll be using in 3DSMAX to cut into the elevator cube. Also the texture is just obviously a placeholder.
EDIT: here is the 3DSMAX solid basic foundation complete and to scale. Depending on the EBE dimensions work I may have to make some adjustments.
Does the EBE use the same scale? 100 cubical inches (254cm | 8' 4") ?
I'm currently just using my custom Segment Builder I've been working on which utilizes old FPSC files.