If the 4th faction is crashing when you're playing it and not when the AI plays it, then there's definitely something wrong with it. Probably something that you're activating that the AI doesn't. To check, just build one of everything, ships structures, planet upgrades... Then select each thing individually and select all of it's options one at a time. From experience whatever you last clicked on before the game crashed is the most likely offender since you're forcing the engine to work with that ship/structure/buff/ability. However!
Something to consider is if you're playing Diplomacy with your graphics being up too high. Sins is only a 32bit program so it's only allowed to use 2Gigs of RAM, high graphics selections tends to make the game crash 5 to 10 minutes in depending on how quickly everyone builds up. Adding a 4th faction is sure to get you there faster then just modding the originals. So if you haven't done that, do it before you do anything else and you'll see the crashing time extends to much longer in between or stops all together. Even at not so high settings, you've added a lot of resources to get preloaded so maybe try out your testing with the settings on low and skyboxes and bloom turned off. Basically do whatever you can to help your system not hit the wall, especially while testing.
As for the weapon points, if your entity files are only saying there's one weapon and your meshes are showing points for unused types, especially for some where there's 11 and 12 points for a weapon, then yes, that's a problem because you've got references to things that don't exist. If the engine can't find a file, it'll search and search and search, and never give up giving you a memory leak until you hit the limit and crash. If it's got references to things that don't exist, it slows down trying to figure out where they are. So whenever you change something, you want to change every reference to your original change as well no matter what file they're in. Aside from reducing the leaks, you have files that are cleaner better prepared for future changes.