I think the stderr.txt file would be of more use. It's generally where I look. I had a similar problem the other day with a credits.ini overflow. Most things, (like # particles in weapons) seem to just stop loading at some point if you overload them. I spent a long time looking for that error with the credits.ini. My suggestion would be to remember every seemingly silly thing you altered (credits.ini crashed the game only when I tried to fire up a simulator or a game, but not on the intro screen) and then look in the Engine Limitation on The Modmaker's Guide:
http://www.digital-eel.com/modguide/engine_limits.htm
This is, at least, a start.
Also if you're having problems with the particle effects, the way I got my brain around them was to start with a weapon I wanted to make, and then strip out all the EMIT bits from the template weapon, leaving only the initial projectile part and its sprite. Then add more in one at a time.
I am not the expert on this, but I don't know of any way to load fighters without a fighterbay. If you figure out that there is a way, tell me about it. I could use it. YOu can do the following (which is in a weapon I have in my mod, but don't plan to release): Essentially make a version of the particle vortex cannon, only limit its firing arc, set it to homing, shut off spin, and replace the beam with a gun. It works well in some respects. YOu can make a drone that will turn and run down point defense rather well, and go up against fighters. The downsides are these: If you make it shootable, it'll last 3 seconds (though you can make it shootable, and make the target something really small SIZE 3 for example) because it can only endure one hit from anything. If you don't make it shootable, it's less realistic, but it'll gain you some fighter time. The next problem is more serious, though. If you don't make it "nocollision" it will fly straight to a cap ship and crack on its hull. Putting nocollision on them seems to defeat the point to me. You can stall this with prefpdef and preffter, but that will only buy you so much time.
-Jeremy