Well, I would have guessed it was another gunboat encounter, even though you never see them in the game they are set up all over the place, but if you fixed the gunboat encounter ini files that shouldn't be happening anymore.
Tracking down a problematic encounter or loadout is a pain in the #$@%! All I can offer you is a method I used when I got hit by a few in my mod...
Go to the system file for the system where you are getting the most crashes, in your case ku02.ini I think? Do a search & replace on the entire file replacing every instance of:
faction =
with this (note the semi-colon):
;faction =
That will essentially disable all of the encounters in that system since there will be no faction using any of them no ships will spawn. Load it up in the game, fly around the problem area and see if it crashes even with no encounters, if it doesn't crash we're on the right track, if it still crashes you need to check things like solar loadouts and errors in the system itself.
Now, go back into the system ini file (ku02.ini) and enable the encounters for one faction, again just search & replace to find this:
;faction = gd_bh_grp
and replace it with (no more semi-colon):
faction = gd_bh_grp
That will re-enable all of the encounter for the bounty hunters only. Load it up and fly around in there for a while, if it doesn't crash the problem is not the Bounty Hunters. If it does crash then the Bounty Hunters are part of, or the entire, problem. Make a note that the Bounty Hunters caused a crash and go back into the system ini file as described above, disable the Bounty Hunter encounters and enable them for another faction, repeat this process until you have covered every faction, one at a time, in that system.
Now the fun part...
Now you have to go through every file that could possibly be causing such a crash, it helps when you know exactly which files have been edited and what was changed in those files since it is the result of something that was changed. The only help you'll have here is that is the crash occurred with more than one faction you can look to see what those factions have in common and substantially narrow your search from there. Remember to check everything, loadouts, faction settings, equipment architypes... it's like searching for a needle in a stack of needles