I think this is one of those instances when a jig is just going to complicate things. Assuming the tube ends are square with the sides, placing them vertically on a flat surface with the centering rings in place squares everything. The flat surface is the jig.
My design uses 4.25" motor tubes, with the forward CR .125" from the front of the tubes. The aft CR is 3.5" behind it (length of the TTW fin tab), .375" from the back end of the tubes.
With rings on the tubes, I place the tubes vertically on my work surface (parchment paper taped flat on a cutting mat, on the table), with the front end of the tubes down, forward CR flat against the paper.
Next, I apply a fillet of Elmer's wood glue around each tube where they meet the forward CR (still flat on the work surface.) Then I carefully lift the assembly and place three small scraps of .125" balsa under the CR, positioning them so the tubes will drop between them. Then I place a 2"x2" piece of flat balsa on the tops of the tubes and gently push down until they are flat against the work surface, which brings the aft CR up .125" (the height of the scraps), smearing the glue nicely between CR and tubes.
Now the flat-surface 'jig' comes into play. With one hand holding the now-glued CR flat against the balsa scraps, and the other hand applying downward pressure with the flat 2x2 on top of the tubes, I rock the tubes ever-so-slightly until I feel the tubes bottom out squarely on the work surface.
Then I place a smallish weight (D-cell battery) on the 2x2 square to keep everything steady, and let the glue dry. The table keeps the tubes square with the bottom CR (which is actually the forward CR), and the top CR (aft), which has been loosely placed a quarter-inch or so from the top of the tubes during this process, keeps them properly spaced from each other.
Two or three hours later, I can glue the aft CR in place, knowing that everything is square with the world.
Having said all that, I realize the only thing more complicated than a jig can sometimes be, is my explanation of how I will do this without using a jig.
Anyway . . . yeah, it works in practice. Now to glue it up.