I don't know what to say here, I'll just write everything I've done so far, it is going to be long and boring though.
I started off with Vortex, everything worked fine, weapon replacers, AFT, the mod that turns the commonwealth into an overgrown forest, FallUI, and a handful of mods that were small QoL for immersion. All quest markers showed up for SS2 until I ran into Carne Asada who wouldn't even prompt the quest, he just tells me something about his stash of chems being taken. I googled around, found out AFT messes up most people's save with SS2 so I uninstall with the instructions provided in that guy's mod description. Problem still persisted, I assumed there were loose files so I deleted that save and started anew. Everything worked fine again, Jake (as a stranger) is marked and then Concord is marked. In the middle of this save, I installed LIGA because it was a lighter version of AFT and there were some posts saying there were no issues with it. One of my residential buildings began to not even finish building after a few hours with that mod added. I refresh it like 10 times and still no luck so I destroyed it. The sound of hammers and saws still kept going and the scaffolding wasn't disappearing. I assume it had anything to do with companion and sorter mods so I uninstalled all that and started anew again. This third save, I noticed there were no quest markers on Stranger and after building and talking to him about Concord, no quest marker showed up at all. I continued thinking it would fix itself and then after he calls me on the radio frequency to meet him at the ampitheather, there was still no quest marker. I don't even fucking know where that is by heart so there's no way I can start Hub of the Problem if I don't know where he is. So again, deleted that save and this time, uninstalled Vortex and nuked my FO4 files before reinstalling. I've been on Mod Organizer 2 now, I went two days straight learning about goddamn LOOT, fucking xEdit, and the mod cleaning bullshit. I reinstalled my mods, that didn't involve companions, just the modern weapons replacer, FallUI sorting, and in-game soundtrack replacer. It worked! I was so happy to see the green little blip on Jake and then Concord but I had to go to work that day so I saved and quit after Jake requested to head to Concord with him. I come back home, load up the save, quest marker is gone. I came here to this forum for help, you all truly did try to.
Again, I appreciate all the answers so far, I'm just frustrated that I don't know what the hell this game wants from me after getting a fucking Harvard's degree in Mod Organizer 2.