I don't exactly know where to start with this issue because I don't fully understand the problem.

Sometimes, eventually, the game starts dropping in fps A LOT. I've found this happens when I bring in something from another mod. But not always, and not immediately. Sometimes it is immediate but rarely. And it doesn't matter if I destroy/kill/send back everything that is modded, the lag persists. And I'm takling a drop from 30/40 fps down to 10 or even 5, its pretty awful.

I know this is vague but like I said I really can't seem to reproduce it accurately. The only thing I do know is that it only happens once I've brought in something from a mod.

And it doesn't matter what mods. I've tried a bunch of them some seem to have a higher chance than others but they have all done it at least once.

Mainly what I'm getting at: has anyone experienced something along these lines? Maybe I should reinstall CC.

A lot of B26-compatible mods have been broken by B27. You'll have to wait until people update them.
You can check the console when you experience low framerates. (Press the ~ key ingame.)
You'll probably see a crapload of lua errors dancing around in there.

Yeah, I figured out that the unofficial Crobotech update caused that for me.

For some reason attatching AI to actors causes 99% drop in frame rate, too many errors.
Might just be the default A though. Happened when I tried to use the un updated War to end all Wars mod.

I've experienced this with mods that claim they have been updated to B27. I'll check the console and see what's there.

The CastMORay and CastObstacleRay functions got updated with a new arg telling them which team to ignore in B27. Any lua-based AI files from B26 or earlier that use those functions for line-of-sight/target acquisition are going to break horribly.

I think that you meant that because of units not killing their allies, the outdated mods use weapons that don't "not kill their allies". That's why I'm sticking with the vanilla mods here.

No, I mean exactly what I say. Most unupdated weapons are fine, because ignoring friendlies is the default behaviour. You don't need to change anything about weapons unless they're scripted and those scripts use CastMORays or CastObstacleRays. DarkStorm's lasers are an example of a pre-B27 weapon that will need fixing.

The problem is, as I said, that the AIs are trying to do their line-of-sight checks... and their scripts lack the necessary values to tell those checks which team to see through. This causes the Lua console to spam a ton of errors, seriously slowing down the game.

For me, the SAW mod lags and sometimes even crashes my game, although that might just be a result of my crappy laptop.