I would check to see if all unit types in the convoy have been properly cloned. All units and parts need unique hex ID's; this was a main cause of crashes with early SH3 and SH4 mods.
I think Jeff Groves has a duplicate ID detector so maybe PM him. Or you can re-clone every modded ship's DAT, ZON, etc. using Silent3d Editor. It's very easy, just tedious.
Maybe gradually remove modded ships one by one until you find one unit that's causing issues...(?)
Another issue that can cause CTD's is using textures larger than about 2048 x 2048. I found that land textures bigger than 2048 crash the game after about 15-20 minutes, maybe the same is true for ship skins and environmental textures (like for sea foam, etc). Best of luck.
