Continued to tweak and adjust the organization trays I have been working for X-Wing, and I think I have a solution design at this point. Ended up not being as thin as I had hoped, but everything fits, and more importantly, the upgrade pieces connect well. Going to test it out a bit in an actual game or two, after I get a chance to print out a few copies, but I am liking it already.
In some ways, it may be better to move to tokens to the left, and make the height equal to the ship card, but I know that will also stretch out the overall piece (with upgrades) much further to the right. I did consider perhaps a slot on the left for each of the upgrade cards, but I doubt such a large space will be successful with the bridging. However, that would allow for the charge icons to overlap in the same space.