With a limited size your cnc can handle you still can make a large base for gluing/assembly.
Say your max capacity is 300 x 300 mm but you are going to make a 900 mm model. Drill 4 holes in a square pattern simultaneously on the base assembly and your assembly jig. You will be drilling your CNC base at max capacity but your assembly base will be a lot longer. Say more than 300 wide by more than 900 long,
Drill only the 300 x 300 mm pattern on the upper portion of the base jig. Remove from CNC and place 2 locating pins on the upper portion of the CNC base. Mount the long assembly jig in the CNC base. This time, only the two LOWER holes will be secured/aligned with the pins.
Reprogram the machine so that only the two lower holes will be drilled in the assembly jig. Remove and step again the mounting process. Repeat until you get the at least 2 rows of holes x 3 (or whatever length). Now you have a base with that you can fit your sub assembly. Just add locating pins.
Make a sketch of what you are going to do.
For the blocks, drill two holes in the same spacing but in the center of the 300 x 300 mm pattern. When you put the blocks on the assembly jig, it will align and fit perfectly.
This is a project I am working on except that I will build a 3 axis CNC with a 360 x 1,000 mm capacity. I have the electronic parts, stepping motors, and the router but the big aluminum extrusions are so damn expensive.