What I've done is take a small shoe box that fits inside the big box (after removing the insert) and I've managed to get all the minis except the two Star Spawns in there. Then I've packed in a few pieces of tissue to stop the minis moving around too much during transport.
It doesn't look particularly elegant but it's certainly worked a treat so far.
Nice! My copy gets to my door on Thursday. Been giving myself a headache just thinking about how Im going to store everything. Ive never made any sort of foam core insert, or anything. Someone on here did message me some really amazing plans for a foam core insert, though...
I prefer to not have to get "artsy and craftsy" to store my game. So I think finding a small shoe box, or couple small like boxes will probably be a winner for me. With the tokens in Planos and the tiles...well...maybe baggies for those.