So it seems that gun mount positions defined in a shipdef file don't seem to match up with positions on the model when viewed in a modelling program, and its making it hard to position them. I've read over the code this morning and I can't obviously see why, but I'm also no good at driving Blender, so its hard for me to test. My suspicions is that the positions are or aren't being scaled correctly when being converted to view space for draw, but I'm really not sure.
So I want to tackle this from two angles.
The first is for someone to determine exactly what's going on. I've made a patch that draws the player ship in wireframe and then highlights the gun positions, like so:


Green is "front", red is "rear". Yellow is actually green, its just what you get when you blend it like that. Its a hack job, remember :)
For Windows users, use this replacement executable (against 201309.32). Anyone building for themselves, build robn/gunmount-debug (or ask me if you want a Linux (32 or 64 bit) or Mac build, and I'll see what I can do). So hopefully that will make it easier to figure out what's going on.
The other thing I want to do is turn the mount points into named positions. But again, I don't know how to drive modelling software to change our models to do that. So, can I get someone to make me a model (existing or new, I don't much mind) with two points "tag_gunmount_front" and "tag_gunmount_rear". Orientation will be important! Once I've got that I can use it to do the code and then hopefully we'll never have to do gunmounts in shipdef files again. And then we can give the cockpit camera position the same treatment too.