I'm not exactly sure of what you are saying, but it sounds like there are two wing joiners: A main one in the center of the wing, and a smaller one near the rear.

If it were me, the first thing I would do is mark a line at the center of the "V" - that is, not the center of the brace, but the spot where the angle changes.

Next, slide one end into one wing. Does it go in all the way to the line? Does it stop right at the line or go a shade past it? Now, remove it and insert the other end of the brace into the SAME wing and make the same observations.

Repeat the above with the other wing half. You may find that the longer end only goes into one side. If so, it may have been designed this way, so cutting the two sides even might be a mistake.

Next: When the braces are added and the wings are together, do they meet fully or is there a gap? If there is a gap, then I would remove just enough material from the longer side to close the gap.

If the two wings meet (no gap) but one wing is higher in the rear than the other, the next question is: Can you align them by putting finger pressure on them?

If they will align easily with only a little pressure, I would epoxy the wings together, but use no glue on the aft 3" or so. Then, before the epoxy cures, glue the aft ends together with medium CA, hold them in alignment and use kicker to cure the CA.

If the to halves will NOT align easily, the next thing to check is: Does the rear joiner seem to be the culprit? Can it be sanded to remove the pressure? How thick are these joiners? Can you sand the top, front and bottom, rear of the MAIN joiner so the wing can rotate a little with less pressure? If you can, do so and glue the wings together as I described above.