Been along time since I used SFC 3, but I am sure some one here will be able to help you.
The problem is either some thi ng is wrong in one of the files, that requires a patched game or the Dynamic model is not being made. If it is the model issue you have to delete the one in the folder and let your PC make a new one.
I just don't remember the name of the file
Most common are:
{modelname}.gf
{modelname}.x
But usually, the most common reason for a crash is an improperly loading mesh. Easiest test would be to backup your custom ship and replace it with a stock one., renaming it to the same name as your custom ship. Does the game then work properly? Also, a SFC3 ship should usually have:
{modelname}.mod
{modelname}_brk.mod
{modelname}.gf
{modelname}.x
{modelname}_brk.x
{modelname}_VL.bmp
{modelname}_TI.bmp
{modelname}_BS.bmp
and then the ship texture files. The .GF file loads the UI for the ship, that needs to be there. The *_??.bmp files are shots of the ship ingame for the interface. The .X files are dynamically generated (usually) if the ship doesn't have them, and without the .mod files, you have no ship mesh to display ingame.
This is where I'd start with your ship... after that, it's how you added the ship into the game..