I don't understand, am I missing something? Most of these parts don't fit with their associated sets and even with ultra-fine adjustments require excessive amounts of tweaking to look somewhat normal. Every piece I've placed is off-center and doesn't line up with the part it's supposed to be connected to and trying to move it into place is tedious at best.
For example, the "glass" pieces for the bridge and CIC superstructure don't even fit the windows of the associated structure despite my best attempts at adjusting the scaling at the finest increments.

Am I doing something wrong?

i could kiss you right now. we've needed this for years.

Beautiful :)