It sound to me you are modding to many files without enough testing as you go. If I change 1 line in a file I test it with the Dev.exe which will stop the game at the problem point and give a sometimes cryptic report but if I only changed a little thing its easy to find.

Do you  use the Devs?

Edit: I think the outside grav well has to do with firing ranges. In SOA2 they wrote a post on it. The ships will want to fire from there farthest point or something like that.

1.  I'm not sure on this one, but might it have something to do with the role types or statcount types that you've placed on your ships?  I know certain types prefer certain targets and such, but I don't recall the AI ever choosing not to attack.  I say take a look at the entity file for ship and compare it directly with a entity file of the same roletype (long-range frigate to long-range frigate, for instance) from whichever version of stock Sins you're modding for. 

I've known shield mitigation to rise so high that the AI will stop firing a ship.  You might also check the weapon type versus armor type (Anti-Light, Anti-Heavy, Light, Heavy, etc).  I don't think that's it, but there might be something in the game constant file you messed up by accident.

2.  I think gruntmaster pinpointed the problem here.  To be honest, I didn't know they could spawn outside of the gravity well, though.  I thought they just came from the center of the ship when no hangar point existed. 

3. Continuous movement away from the gravity well does indeed have to do with the weapon ranges.  The first line below your weapon entries is "m_weaponIndexForRange X" with "X" being 0, 1, or 2 (a reference to the weapon index or hardpoint.  The ship will move to the maximum range of whichever weapon type you enter here before it decides it wants to turn and face it's pursuer.  So, if I choose to have my ship use all weapon 1 hardpoints (or the second weapon entry), which has a range of 4000, then my ship will attempt to move 4000 units away from its target before turning around.

Unfortunately, the fastest way to do this is a straight line that inevitably leads out of the gravity well.  If the pursuing ship is the same speed or very close to the same speed, that capital ship of yours will just continue running unless you give it specific orders to attack.

I'm still experimenting with it in my own mod, but I've found that it usually occurs when the pursuing ship does NOT have fighter-style movement enabled and is faster or similar in speed to my ship.  Or, if both ships have fighter style movement and the same speed.  If my ship is faster everything works out.  I'm still working on getting models with textures into the game for the first faction, but I believe that once all ships have fighter-style movement I'll be able to jimmy the speed values to reduce this problem to a rare occurance. 

1. If a new race doesn't have certain StatCount types available to it, you get this problem. In general try to have one ship comparable to what the regular Sins ships can do.

2. You can open the mesh file in notepad and add a hangar point manually (careful with the spelling). I usually just find the "Center" point, copy it, paste it, change it to hangar, and update the count at the top.

I have gone through and made all the ships using strike craft have a Hanger point reference in the mesh file.  Thanks so much for this tip, as well as how to accomplish it, as a lot of those ships did not have this, and I had very frequent spawns way outside the gavrity well.

I have a bunch of differing factions, but two of them were not using all the statcount types.  I had initally ensured that all the role types were there, with one ship having two types to make up for a mising ship, but not so the statcount types.  This has been corrected based on the feedback you guys have given.

My MOD is more focused on getting certain model meshes with the appropriate weapon effects for those models.  As such, I am relying on the original game's balacing and research.  So, I didn't change the original weapon types and stats much, but I did change the weapon effects so that it will look how it should for the ship model used.  As such, I may have a weapon Type defined as Projectile, but it's effects would use a beam weapon stats.  There are not any apparent problems doing it this way, but I could be wrong, and it may also be the culprit that is causing the ships to just stop firing after a while in some instances.  

On the firing range bit, and how it affects the fighter style movement, I will have to do trial and error with it I guess...  Messing around with the ship speeds and attack range until ships running away from the other is minimized or resolved.

Again, thanks for all your help and feedback, guys.  It was very userful.