I've gone for a custom case, an old Kenner Star Wars action figure carry case.
I carved up the inside a bit to make spaces for the tokens. Most are still in bags, but I want to get some little plastic cases and fit them with foam into the action figure slots. I had to carve up space for the pilot cards and asteroid tokens. I custom made the holder for the movement rules.
Finally the deeper side got a layer of foam board with holes cut into it and the original plastic carry cases inserted into those spots.
There is still room for more ships. The top is reserved for the Falcon.
There is still some work to go on the case. After seeing the KR Foam I want to fill up one side with that to make it easier to swap contents (if I ever get enough ships). I also need to reduce some of the width, the lid for the miniatures and the foam with the movement rulers makes a really tight fit and I don't think the old plastic tabs can take the strain for to much longer.
For those who think it is the end of the collectors world to carve up an old 1980's case like this so did I. I had one that I threw out earlier in the year (gasp) because the tabs were broken and it was in a state not worth keeping. It was an original 1980's case. Then X-Wing comes out and I decided it would make the perfect carrying case. I hit the second hand markets and found one. I get it home to discover a copyright 2004 mark inside of it. This is just a rerun to make money, so I had no qualms of carving it up!