Well I have tried that, to no effect still the same problem. but I am doing the manual way now.
In regard to your ship, ohh, I thought I answered you, it must have been one of does "POFF" I thought I did that

. sorry, must have had my head into the Lucifer by then. "Me looking in his to be sent later box". Yes there it is. I might as well write it here.
But here is what I discovered.
First off all, you have those HUGE barrels, and your paths are located above along the Y axis "in FS1/ FS2". Make it more diagonal, to prevent AI to fly into the ship. AI will Almost certainly fly into large sticky objects, even on the Lucifer’s wings as i discovered. a diagonal approach vector minimizes this, remember AI will Always go up or down to get out of the way, the AI don’t have a "this did not work, lets try another direction" function. If it has it is Very very ineffective.
And the rest of your paths are way to bound to either the X,Y or Z axis. Make them more diagonal. I know that the FS2 modellers at volition have done the same thing on some of the FS2 models. and not surprisingly, The AI will do the same thing on models such as the hecate. That thing was built in haste IMHO. Even the paths on the Orion are FUBAR. Just look at them from inside FRED2.
Also, i suspect the game of not setting an Collision bounding box for Rotating objects such as barrels, Rader dishes.” Remember the Knossos, is what I use to think, when putting in paths."
The knossos is one Huge rotating thing, still the AI don’t try to avoid it, meaning that there must be no bounding box, Why, because there are no "Fixed" objects. OR volition removed it somehow. Again this is just educated guess. A collision-bounding box would also make the Ai avoid the centre of the device, and we don’t want that do we.
to the problem why your ships fly of in the distance when attacking a turret, I never saw that.
The one Model you should look at from volition is the Arcadia. It only uses two points in paths for turrets, and this works fine. But even this model has some odd paths. Maybe they are a mistake; maybe they are put in like that for reason. I don’t know.
But maybe minimizing the number of points in your turret paths may solve this fly off problem, and even the collision problem. The Arcadia has no more than 2 point for turret paths, simplicity itself, and I’m sure FS2 engine like it simple. So keep it simple stupid is my rule when I put in paths.
Regarding the clipping, It clips be sure of that I saw this on several locations. But even the Lucifer is clipping when you have a really close look at certain angles.
You need to triangulate the model. The fs2 engine is designed to show models built in 3dmax. 3dmax triangulates any models by default, sure you can have polygons above 3 points in max, But they are still triangulated and you can see this if you select properties and deselect "edges only" I have stated this before and I state it again now. 3 or 4 points per polygon or you will have clipping. Above 3 point polygons should only be used when two surfaces of 3 points that shares two of these are completely flat when joined. I suspect that Volition To POF converter plug in for max discards unneeded points in order to optimise the model.
It is an extreme viewing angle combined with bended surfaces. ("A 4+ point surface") that causes clipping. The smallest 3 dimensional surfaces you can view on a PC Screen in 3 dimensions is consisting of 3 points. And you simply can’t bend a 3 point surface, so unless you are 100% sure that a surface of 4+ points are flat. Make the surface triangulated.
Hopes this helps you in some way.